Fundamentals of BIOVIA Pipeline Pilot

Copyright2008, Accelrys Software Inc. All rights reserved.
Biological Sequence Analysis Using

Accelrys Pipeline Pilot
Pei-Li Li
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/ Accelrys
Pipeline Pilot Training Course

Fundamentals of Pipeline Pilot
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Outline
Introduction and Overview of Pipeline Pilot

Components and Protocols
General Data Manipulation and Filtering
Introduction to Subprotocol
Introduction to Web Port Interface
Introduction to Sequence Analysis Collection
Q&A
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Overview
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The Power of Pipeline Pilot
Cl
Clean
Suspect
S
tD
Data
t
Real-Time Calculations
Multiple Data Sources
Data Reduction
Write Output
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What is a data record?

A data record is the
smallest data unit in
Pipeline Pilot.
Pilot
It consists of a
hierarchical structure of
property name-value pairs
and may include a
molecule object.
data properties
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Sequence object
What is a Component?
A component is the building block used
to create workflows
Each component performs a task like
reading, writing or manipulating data
Components can have one input and up
to two output ports
Highlighting a component displays its
parameter panel which control its
behavior
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What is a Pipeline?
A series of components connected through pipes
through which data flows.
Each component acts on the data and passes it on to
subsequent components.
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Data Flow in a Pipeline

access.
Seq
File Reader
Molecular Weight
Notepad Viewer
Reads data records

from flat file
Calculates MW and
adds to record
Displays records as
rows in NotePad
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What is a Protocol?
A protocol consists of one or
multiple pipelines that are
run sequentially.
Components are executed
left to right, top to bottom.
Pipeline 2 will not start
processing data until
pipeline 1 has completely
finished processing all the
records.
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MolW
Y13255 TGGTTA 187216.8

Y13260 TCTGCT 177200.4
Y13263 CAAGAA164098.6
>gi|2695850|emb
>gi|2695846|emb
>gi|2695852|emb
TGGTTACAACACTTTCT
TCTGCTGGTTACAACAC
CAAGAACCACAATACTG
TCTTTCAATAACCACAA
TTTCTTCTTTCAATAAC
CAGTACAATGGGGATTT
TACTGCAGTACAATGGG
CACAATACTGCAGTACA
TAACAGCTCTCTGTATA
GATTTTAACAGCTCTCT
ATGGGGATTTTAACAGC
ATAATGACAGCTCTATC
GTATAATAATGA...
TCTCTGTATAAT...
AAGTGTCCGGTC...
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Pipeline Pilot Main Window

Additional tools
Search Bar
Favorites
Pipeline
Explorer Window
Component
Protocol
Task bar
Status bar
Parameter Panel
Help Text
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Menus and Toolbars
Finding Information in
Protocols
p
Scale drop-down
Zoom by Navigating
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Protocol Task Bar

Quick access to open protocols
Quick access to subprotocols
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SciTegic Help Center

Single point access for
users/admins/developers
But, customized pages
for different types of
users
Google-like searching
Quick access to glossary
Quick access to
reference help (e.g.
PilotScript)
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Explorer Window
Consists of four tabs
User, e.g. Joe
Contains all protocols and components
for an individual user
Protocols
> 900 realistic examples provided by SciTegic
To be used as-is or as the basis for more complex
protocols
Shared by all users
Components
> 1600 different components provided by SciTegic
Grouped in distinct categories
Shared by all users
All
Everything from User, Protocols and Components
tabs
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Client-Server Architecture
Server runs protocols
Server accesses databases and
files
Visualization apps open
temporary files on server
Limited transfer of data
between client and server
Files that are not on server
need
Excel
Cli t
Client
UNC
File server
UNC path
Be made sharable
ODBC
Recommendation
Database server
Create sharable folder on

client
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Pipeline Pilot server

Developing a Protocol
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Running an Existing Protocol

Examples available in Protocols tab
To run an example protocol
Double
Double-click
click a protocol in explorer
window
Execute by clicking the green Run
button
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Executing a Protocol
Run
Start execution (F5)
Stop
Interrupt execution
Errors
Flag indicates where
execution stopped
Last error message will be
available until the protocol
is edited
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Creating a New Protocol

1. File/New (Ctrl-N)
2. Add component(s)
3. Connect
components to
form one or
multiple pipelines
4. Run
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Handling Components
Components can be dragged into a
pipeline
It will try to connect when placed to the
right of an existing component
Red components have one or more

required parameters that need to be
set
Components can be inserted into
or appended to a pipeline
Double
Double-clicking
clicking a component in the
hierarchy window will automatically
position and connect a component
Right-mouse drag replaces components
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Handling Connections
Connections can be made by dragging
from a fail or pass port of component
1 to the input port of component 2
Connections can be deleted by
selecting them and pressing del
Double-clicking a connection
toggles between pass and fail
Multiple inputs/outputs are allowed
(branching)
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Reusing Component Information in Protocols

Using Ctrl + V :
If a Component is
selected
If a Pipe is selected
If multiple Pipe are

selected
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Anatomy of a Component
Highlighting a component displays its parameter panel

Required parameters shown in red
Optional parameters shown in black
Parameter Groups can be expanded/contracted by
clicking on the + or - icon
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Parameter Grouping
A Group is a way to organize
parameters into categories
Parameters in a group behave
as standard parameters
The parameter that is the
group heading can either
accept a value or not
depending on the parameter
type (GroupType accepts no
value))
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Documenting a Protocol
1. Editable captions for
each component (highly
recommended)
2. Sticky Notes
3 Documentation for individual
3.
components accessed by rightclicking on the component and
choosing Edit
Purpose
Description
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Component Help Text

Purpose
One-line component description displayed as fly-over help
p
Description
Paragraph describing usage of the component and data streams
Input, pass, and fail
Help text accessed by right-clicking on a component and choosing the Edit

option
Help text can be changed and saved. Native components must be renamed
when saved
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Sequential Execution
Non-connected pipelines are executed one after another
Last record in pipeline 1 will be written to the output file before
the first record is read in pipeline 2
When records are read in, they move as far to the right as possible
Data can be shared between pipelines using either files or global
variables
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File Browse
User Defined Shortcuts

(these can be renamed by user)
Server Defined
Shortcuts (additional shortcuts
can be defined by the administrator)
Collection Example Data
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Component Disabling
Component disabling
Right-click on
component and
choose Disable from
menu
Options
Pass Data
Fail Data
Halt Pipeline
U
Use F10 k
key tto ttoggle
l
between options
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Exercise 1: Introduction
A. Find the example Aligning Sequences and run it
B. Use a FASTA reader to read in O43291.fa. Calculate
the sequence molecular weight and display in an HTML
table viewer. Place a checkpoint on one of the
components.
C. Read the first 100 records of the
NRDB_nucleotide_10K.fa file and display the results in
an HTML table viewer.
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Components
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Component Collections
Components are organized in folders based on their
component collection:
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Component Types
Within each collection,
components are organized in
folders based on functionality:
Reading
Writing
Viewing
Filtering
Manipulating
Calculating
Etc.
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Data Reading
Generic file readers include the Delimited Text Reader,
Excel Reader, XML Reader, HTML reader
File readers are available for most popular molecular
and sequence formats: SD, MOL2, SMILES, PDB, FASTA,
etc.
Database readers can read from any database format
via ODBC
File readers support: zip files, multiple files (use Ctrlclick to select), wildcards (users\myname\*.txt).
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File Browse
User Defined Shortcuts

(these can be renamed by user)
Server Defined
Shortcuts (additional
y the
shortcuts can be defined by
administrator)
Collection Example Data

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Data Writing
Generic file writers include the Delimited Text Writer,
XML Writer, HTML Writer
File writers are available for most popular molecular
and sequence formats: SD, MOL2, SMILES, PDB, FASTA
Database writers can write to any database type that
supports ODBC connections
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Data Viewing
Viewers run on the client, and third party applications
need to be installed on the client machine: Excel,
Internet Explorer,
Explorer Spotfire
Charting viewers are available using Excel and/or the
Reporting Collection
Dialogs can be used to ask for user input at run time
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Sequence Analysis Components

File Readers/Writers
Pattern matching
EMBL
FASTA
GCG
GenBank
Swiss-Prot
Online Fetching (from NCBI)
Similarity search
Local BLAST search
Online BLAST search (at NCBI)
Prepare BLAST database
(formatdb)
Smith-Waterman
HMMER
The best way
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PROSITE
Regular expression
GC rich regions
Open reading frames (getorf)
Masking (seg, xnu)
Signal peptide sites
Restriction enzyme sites
Proteolytic sites (digest)
Alignment
Multiple Sequence Alignment
(ClustalW)
Pairwise local alignment
(water)
to find components is to use the search functionality (Ctrl-F)

Sequence Analysis Components

Calculators
Utilities
GC Content
Molecular Weight
g
Isoelectric Point
Protein structure
Secondary structure
prediction (garnier)
Predict transmembrane
proteins (transmem)
Reverse complement
Transcribe
Simple translate
Six-frame translate
Back translate
Generate subsequence
fragments
Viewers
Sequence
Oligos
siRNA duplexes
Find & match primers
Artemis, plain text, or

custom report
Alignments
JalView, plain text, or
custom report
BLAST results
The best way
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to find components is to use the search functionality (Ctrl-F)

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3rd Party Tools

Integration flexibility illustrated through inclusion of:
Languages
BioPerl (e.g., file readers, writers, program execution)
Perl (e.g., PROSITE)
BioJava (e.g., isoelectric point)
Applications
EMBOSS (e.g., garnier, getorf)

BLAST (NCBI)
ClustalW
GCG (e.g., seg, xnu, & transmem)
Note: All the above listed third-party tools are included as part of the
Sequence Analysis component collection. You do not need to install
any additional software. For EMBOSS, BioPERL, and BioJAVA, while we
only expose parts in Pipeline Pilot, the entire suites are included.
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Exercise 2: Using Components

A. Read first 100 sequences from
NRDB_nucleotide_10K.fa. Compute the sequence
molecular weight and the GC content,
content and view
results in Excel.
B. Select random 5% of sequences from
NRDB_protein_10K.fa. Calculate the Isoelectric point
for the sequences, and sort the sequences from higher
to lower using the isoelectricPoint property. View
results in Excel and display first ten sequences in the
HTML Table Viewer.
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General Data Manipulation and Filtering
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Data Records
A data record is the smallest
unit of data flowing through a
pipeline.
pipeline
It is a collection of data
properties and may include a
chemical structure (molecule).
For simplicity, it can be
thought of as a row in a table.
In general,
general Pipeline Pilot
components process 1 data
record at a time.
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Data Properties
A data property is an attribute of a data record.
It consists of a property name and a property value.
It is preferred that property names contain only
alphanumeric characters and underscores.
Data property values can be numbers, strings, Booleans,
molecular fingerprints and arrays.
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General Data Manipulation and

Filtering
General Data Manipulation
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Property Manipulation Components

Copy Property, Rename Property, Keep Property,
Remove Property
P
Performs
f
the
h named
d operation
i on the
h property or properties
i
listed in the parameter panel of each component
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Define Your Own Property

Create New Property
Creates a new property and assigns each the value specified in
the 'DefaultValue'
DefaultValue parameter
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Counting and Indexing Data

Count and Index Data
Sets an index number (starting at 1 by default) on a data record,
then increments the number so that consecutive records get
sequentially numbered
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Sorting Records
Sort Data
Sorts the data records based on the value found in the data
property specified in the parameter panel
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Tagging Data Records

Purpose
Determine source of a data record
Identify
Id if
reference
f
d
data records
d d
downstream
Substructure Search from Tag
Similarity Search from Tag
A tag is a data property and can be added by

Tag component
SourceTag parameter in any reader
Using PilotScript in a Custom Manipulator or Custom Filter
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Tag Data
Tag Data
Creates a new data property for each incoming record based on
the value entered into the parameter panel
Value for each new data property is set to true
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Reader Components: SourceTag

Each reader has a
SourceTag parameter
Thi
This creates a new property
called SourceTag which can
be assigned one of the listed
values
This allows the direct
identification of the source
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Basic Math
Perform single or multiple property math
Property2 only required if the operation requires two
properties
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Statistic Components
Replace MultiValue Stats and
Moving Average.
Average
Output results as a summary
or on the original data
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General Data Manipulation and

Filtering
General Data Filtering
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Property Filters
Property Value Threshold Filter
This component allows a user to specify
a property
property, a threshold value and a
condition to filter each data record
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Exercise 3: Data Manipulation

A. From Generic data\Tables read in Assay1.txt and Assay2.txt:
1. Tag each record based on the file it came from. View results in an
HTML Table Viewer.
Viewer
2. Filter for only records with the Name A.
B. Filter Generic data\Tables\MicroBeta.txt. Each filter should

generate a separate worksheet in single Excel document:
1. Value greater than 5000
2. Compound equal to Cmpd-2 and conc greater than 2.000e-11
3. Compound equal to Cmpd-2 and conc less than or equal to 2.000e-11
C. Filter the hts_rawdata1.csv file (Generic data\Tables) to display

only records with a Well value greater than P20.
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SubProtocol Creation and Handling
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Why SubProtocols?
Encapsulate complex logic (one or more components)
Implemented with many components
Represented
R
t d as a single
i l componentt
Portable, easy to distribute

Treated as a single component
Input, pass, fail ports
Parameters exposed to the outside
Created using Collapse To Subprotocol menu option
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Creating a subprotocol
1.
Highlight components to be part of subprotocol
2.
Right-click selected components and select Collapse To Subprotocol
3
3.
Create the interface for your component on Promote tab
4.
Choose appropriate icon and ports on Ports tab
5.
Provide new component description on Help Text tab
6.
Change caption for new SubProtocol
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1.
2.
3
3.
4.
5.
6.
Which parameters are useful to users

of this subprotocol?
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Parameter Promotion
Promoted parameter becomes a parameter of
subprotocol
Parameter can be renamed if necessary
From the Promote tab of the Edit dialog:
1. Navigate to the component of interest (Prev / Next buttons)
2. Highlight the parameter of interest and click Promote
3. Parameter now exposed in component parameter list of the
subprotocol
b
l using
i string
i token
k
Parameter Source can be referenced inside the

subprotocol (and its components) using the $(Source)
string token
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1.
2.
3
3.
4.
5.
6.
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1.
2.
3
3.
4.
5.
6.
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1.
2.
3
3.
4.
5.
6.
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Subprotocol Data Flow

Data enters a subprotocol through the first component
with an input port. Only one such component is allowed
Subprotocol output streams are the sum of:
Pass: output from any components pass port
Fail: output from any components fail port
Subprotocol:
Pass
2500 records
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Fail
1518 records
982 records
Subprotocol Utilities
Component
Description
Data to Fail Port
Use the component in a subprotocol to direct records coming out of a Pass port of a
component to the Fail port of the sub-protocol
Data to Pass Port
Use this component in a subprotocol to direct records coming out of a Fail port of a
component to the Pass port of the sub-protocol
Dont Pass Data
Use this component in a subprotocol to keep records coming out of an internal component
from being passed out the subprotocol. (You can also turn off output ports to achieve this
effect.)
No-Op
Use this component to pass all incoming records to Pass port. This is useful inside
subprotocols to capture the point of input. For example, to run an initialization pipeline
before accepting input, use the No-Op component as the first component on the second
pipeline.
Subprotocol
Use this component to define a subprotocol in a pipeline. When you are creating a pipeline
that requires a subprotocol as a component you can drag this subprotocol component into
the pipeline, open it, and add components into it.
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Example
Complex filter (HTS Filter)
Records from pass/fail ports
exit subprotocol through its
pass/fail ports
Pass streams can be turned
into fail streams and vice
versa
Output ports can be
terminated
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Exercise 4: Creating Subprotocol

A. Create a subprotocol-based component that reads a
FastA file and calculates sequence molecular weight
and isoelectric point
B. Extend the component from above to expose the
Delimited Text file reader parameters Source and
Maximum on the parent component
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Webport
http://servername:9944/webport/main.htm
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Webport
Running Webport Protocols
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Webport
Single sign-on
Log-in once
Store credentials locally
Validity of credentials configurable
Auto-launch protocols using

protocol link
http://localhost:9944/webport/mai
n.htm?protocol=Protocols/Collect
data
Jobs window
Multiple jobs deletion
Performance improvements
Java sketcher (to run out-of-thebox)

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Library Tab
The Library tab is displayed when you log in.
Select the protocol you would like to run. The protocols are now in
a tree view to make it easy to see all available protocols at once.
once
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Protocol Tab
The Protocol tab is where you set the parameters for the protocol
and where you can see displayed results files (Each file will have a
tab on the right side of the screen)
The File browsing is greatly improved. The dialog is similar to the
dialog in the client.
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Jobs Tab
The Jobs list is now sortable, by clicking on any column
header. Click the column header again to sort in the
opposite direction.
direction
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Webport
Creating Webport Protocols
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Use Writers
Writers (no Viewers)
Write to the $(runDirectory), $(jobDir) or $(userDir)
No dialogs or pop-ups
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Promote Parameters
Promote parameters that you want visible in Webport
Component Parameters
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Protocol Level Parameters
Save to Web Services

Save to Protocols\Web Services
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Run via Webport
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Questions & Comments

Accelrys Web Site
www.accelrys.com
Accelrys Community
accelrys.org
Accelrys Advantage Knowledge Base and FAQ

customer.accelrys.com
Molecule Scientific Co., Ltd.

www.molsci.com.tw
www molsci com tw
MSC Support
msc-support@molsci.com.tw
02-27132977
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Copyright2008 Accelrys Software Inc. All rights reserved.
Pipeline Pilot Training Course

Sequence Analysis Collection
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Outline
Sequence Analysis Collection Components and Protocols
Data Record Structure
SAC Example Protocols
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Sequences, Annotations and Features
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SAC Readers
Reader components available for
sequences, alignments and profiles.
Many popular formats are supported.
supported
There are also Generic readers for
sequences and alignments, that infer
the format from the file extension.
Users can specify the number of records
to read.
Online sequence Fetchers allow access
to databases even if local copies do not
exist.
For sequence formats that include
features, the user can choose not to
read features.
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SAC Writers
Writers available for
sequences, alignments and
profiles.
profiles
Many popular formats are
supported.
There are also Generic writers
for sequences and alignments.
Users can specify the number
of records to write.
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Reading/Writing Example
Converting a GenBank sequence to FASTA format.
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SAC Viewers
Several options for viewing
sequences, alignments and
HMM (text,
(text Java,
Java HTML,
HTML PDF)
Similarity Search Viewer
output is a PDF
FASTA Entry Prompt
Similarity Search Table Viewer
Reporting plotting tools are
included in the Viewers
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Viewer Examples
Artemis Viewer
Sequence Viewer
JalView
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Aligning Example
Aligning sequences and viewing the alignment using
JalView or JalView 2
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SAC Manipulators
Manipulator component
functions include:
Extracting sequence features
Creating sequence fragments
Producing open reading frames
Translate/transcribe
And more!
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SAC Annotators
Annotator components allow
sequence annotation and
pattern searching
Matches are added as
features to the sequence
data record
Act as filters - Sequences
without the feature of
i
interest
are passed
d out the
h
fail port
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Annotation Example
Annotation of a protein sequence using a variety of
components. This protocol uses BioPerl, BioJava,
PROSITE and EMBOSS
PROSITE,
EMBOSS.
BioPerl
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BioJava
BioPerl
BioPerl
PROSITE
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EMBOSS
SAC Calculators
Property calculators add
sequences physical
properties to the data
stream.
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Plots
Charge
Hydrophobic Moment
GC Content
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Plots
These plots require the Reporting Collection.
These plots can be embedded in a report similar to
other reporting components.
You cannot link reporting plots sequentially in a
pipeline, however, you can combine them using other
Reporting Elements (e.g., Tile Horizontal).
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Exercise 1: Basic Pipeline Pilot and SAC

A. Find all of the sequences with shock in the
description of the sequences in the
NRDB protein 10K fa file
NRDB_protein_10K.fa
(in Sequence Analysis Data\Sequence folder)
1. Calculate the molecular weight of these sequences
2. Filter for only protein sequences with molecular weight
greater than 70,000
3. Perform both of the following:
Align
g these sequences
q
and view the results with JalView or the
Alignment Viewer
Predict their secondary structure and view the results in the
Sequence Viewer
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Sequence Data Structure

Sequence (with properties for sequence data,
identifiers description
identifiers,
description, length)
AnnotationGroup
(no properties)
Annotation (with properties for

annotation type and named values)
FeatureGroup (no properties)

Feature (with properties for feature
type location
type,
location, and qualifiers)
NOTE: All sequence readers (except FASTA) have a
parameter to include/exclude features and
annotations.
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Sequence Annotation Properties

AnnotationGroup (no properties)
Annotation[1,2,3.n]
(Itemizes information from sequcence

file)
Keywords
Comments
References
NOTE: FASTA sequence files will not have
annotations.
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Sequence Data Structure

Sequence data records have the following hierarchy:
Sequence (with properties for sequence data,
identifiers, description, length)
AnnotationGroup (no properties)
Annotation[1,2,3n] (with properties for annotation type and
named values)

Feature[1
Feature[1,2,3n]
2 3 n] (with properties for feature type
type, location
location, and
qualifiers)
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Sequence Feature Properties

Feature[1,2,3n]
(with properties for feature type,
location and qualifiers)
location,
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Alignment Data Structure

Alignment data records have the following hierarchy:
Sequence (consensus sequence)
SequenceGroup (no properties)
Sequence[1,2,3n] (ungapped sequence data)
Annotation Group
Annotation[1,2,3n] (with properties for alignment start
and end)
FeatureGroup
p ((no p
properties)
p
)
Feature[1,2,3n] (with properties for gaps)
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Alignment Data Structure

Sequence (consensus sequence)
SequenceGroup (no properties)
Sequence[1,2,3n]
(ungapped sequence data)
Annotation Group
Annotation[1,2,3n]
(alignment start and end)
FeatureGroup
Feature[1,2,3n]
(alignment gaps)
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Search and Similarity Tools
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Search and Similarity Tools

Includes components that wrap the
familiar programs:
-
ClustalW
HMMER
BLAST
Smith-Waterman
Muscle
Sim4
Similarity Search results are added to

the data records hierarchy.
y
Includes components to write databases
from flat files
BLAST DB Sequence Fetcher brings back
a full-length sequence
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Writing BLAST Database Examples
For sequences already in a FASTA file,

use Create BLAST Protein Database
(formatdb) (or its nucleotide
counterpart)
For other sequence file formats, use

BLAST Protein Database Writer (or its
nucleotide counterpart)
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Using BLAST Output

Extract the resulting database hits,
fetch the sequence data using the
BLAST DB Sequence
S
ffetcher,
t h
and write them out in FASTA format
Display the BLAST results using the
Similarity Search Viewer
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PP-SAC_Lec - 13
Exercise 2: Similarity Search

1. Read NRDB_protein_10K.fa:
Create a FASTA file that contains sequences matched by the

PROSITE Calcium-binding
Calcium binding EGF-like
EGF like domain signature (PS01187).
(PS01187)
Create a BLAST database containing the sequences that do not
match the PROSITE Calcium-binding EGF-like domain signature
(PS01187).
2. Use BLASTp to search O43291.fa against the non-EGFrelated BLAST database ((created in #1).
) Display
p y the
results in the Similarity Search Viewer.
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Similarity Search Data Structure

Similarity Search (e.g., BLAST, HMMER) data records
have the following hierarchy:
Sequence (query sequence)
SearchResultGroup (no properties)
SequenceGroup/HMMGroup (with properties for algorithm,
algorithm version, database name, number of hits)
Sequence/HMM[1,2,3n] (the hit, with properties for
description e-value,
description,
e value score)
HighScoringPairGroup (no properties)
HighScoringPair[1,2,3n] (with properties for
e-value, query and subject sequence alignment
information)
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PP-SAC_Lec - 14
Similarity Search Properties

BLAST Search
HMM Search
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Similarity Search HSP Properties

HMM Search
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PP-SAC_Lec - 15
BLAST Search
HMM Data Structure

An HMM file, and an HMM search (e.g. Search HMM File
with Sequence) have the following data structure:
HMM (with properties for identifiers, description,
length, null model)
PositionGroup (no properties)
Position[1,2,3n] (with properties for begin and end transitions,
match and insert emissions)
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HMM Data Structure

Properties
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PP-SAC_Lec - 16
Position
Data Structure
MAQLCGLRRSRAFLALLGSLLLSGVLAADRERSIHDFCLVSKVVGRCRASMPRWWYNVTDGSC
QLFVYGGCDGNSNNYLTKEECLKKCATVTENATGDLATSRNAADSSVPSAPRRQDSEDHSSDMF
NYEEYCTANAVTGPCRASFPRWYFDVERNSCNNFIYGGCRGNKNSYRSEEACMLRCFRQQENPP
LPLGSKVVVLAGLFVMVLILFLGASMVYLIRVARRNQERALRTVWSSGDDKEQLVKNTYVL
SEQUENCE
ANNOTATION GROUP
FEATURE GROUP
SEQUENCE GROUP
SEARCH RESULT GROUP
GPCRASFPRWYFDVER
NSCNNFIYGGCRGNKN
SEQUENCE(n)
SYRSEEACMLRCFRQ
SEQUENCE/HMM GROUP
FEATURE
ANNOTATION
SEQUENCE/HMM (n)
ANNOTATION
FEATURE
HIGH SCORING PAIR GROUP
2READ
STRUCTURE
PREDICTION
READ
SIMILARITY
ALIGN
SwissProt
FASTA
SEQUENCES
SEQUENCE
SEARCH
SEQUENCE
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HIGH
SCORING
PAIR
Generic Utilities for Hierarchies

Extract
Delete
Reassemble
Versions of these exist for similarity search hits,

sequence features and annotations
annotations, and aligned
sequences
Several manipulators (e.g., Keep Features by Type) use
this pattern internally.
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PP-SAC_Lec - 17
Data Structure
MAQLCGLRRSRAFLALLGSLLLSGVLAADRERSIHDFCLVSKVVGRCRASMPRWWYNVTDGSC
QLFVYGGCDGNSNNYLTKEECLKKCATVTENATGDLATSRNAADSSVPSAPRRQDSEDHSSDMF
NYEEYCTANAVTGPCRASFPRWYFDVERNSCNNFIYGGCRGNKNSYRSEEACMLRCFRQQENPP
LPLGSKVVVLAGLFVMVLILFLGASMVYLIRVARRNQERALRTVWSSGDDKEQLVKNTYVL
SEQUENCE
SEQUENCE GROUP
SEARCH RESULT GROUP
GPCRASFPRWYFDVER
NSCNNFIYGGCRGNKN
SEQUENCE(n)
SYRSEEACMLRCFRQ
SEQUENCE/HMM GROUP
SEQUENCE/HMM (n)
HIGH SCORING PAIR GROUP
REASSEMBLE
SIMILARITY
EXTRACT
DELETE
EXTRACT
DELETE
SIMILARITY
SIMILARITY
ALIGNMENTS
ALIGNMENTS
SEARCH
SEARCH HITS
HITS
REASSEMBLE
ALIGNMENTS
SEARCH
RESULTS
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HIGH
SCORING
PAIR
Exercise 4: More Similarity Search

1. Use BLASTp to find sequences similar to the
tyrosineKinase.fa sequence.
a. Fil
Filter out the
h HSP
HSPs with
i h < 60% sequence id
identity
i
b. Obtain the full length sequences for the HSPs.
c. Align the query and the full length hits using ClustalW, and
view the alignment using JalView or the Alignment Viewer.
d. Reassemble the similarity search results and view them in
table format.
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PP-SAC_Lec - 18

Examples
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Translating and Transcribing Sequences
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Iterate BLAST Calls
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Checking for Novel GPCRs
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Performing Ortholog Comparisons
Rat
Sequences
Compare
using
BLAST,
then
Filter and
Score
High Match
Medium Match
Human
Sequences
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Low Match
Performing Ortholog Comparisons
Identify ortholog pairs across genomes

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PP-SAC_Lec - 21
Finding siRNA Off-Target Sites

genomic
sequence
other
gene
region
target
gene
region
Off-target
siRNA
regions
i
siRNA
regions
g
Correctly silenced gene

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Wrongly silenced gene
Target cDNA
Generate
siRNA
Search predictions
sites
against
genomic
sequence
siRNA
predictions
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Identify and
filter
Genomic DB
siRNA
site locations
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Off Target sites
On Target sites
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Divide and BLAST (DAB)
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Divide and BLAST (DAB)
DAB Subprotocol:
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KEGG Pathway Database

Comprises current knowledge on molecular interaction
networks
metabolic
b li pathways
h
regulatory pathways
molecular complexes
Can be used by Pipeline Pilot to connect genes with

relevant compounds (or vice versa)
Integrated as a web service using SOAP
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http://www.genome.jp/kegg/
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KEGG Pathway Database
GENE
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Integrating KEGG with SOAP
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PP-SAC_Lec - 25
COMPOUND
Find all endogenous compounds related

to a gene target of interest
tynA
Histamine Oxidase
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Find the pathway most related to

each compound of interest
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PP-SAC_Lec - 26
Questions & Comments

Accelrys Web Site
www.accelrys.com
Accelrys Community
accelrys.org
Accelrys Advantage Knowledge Base and FAQ

customer.accelrys.com
Molecule Scientific Co., Ltd.

www.molsci.com.tw
www molsci com tw
MSC Support
msc-support@molsci.com.tw
02-27132977
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PP-SAC_Lec - 27

Fundamentals of BIOVIA Pipeline Pilot

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Fundamentals of BIOVIA Pipeline Pilot

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Biological Sequence Analysis Using

Pipeline Pilot Training Course

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Introduction and Overview of Pipeline Pilot

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Fundamentals of Pipeline Pilot

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The Power of Pipeline Pilot

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What is a data record?

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Data Flow in a Pipeline

Reads data records

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Y13255 TGGTTA 187216.8

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Pipeline Pilot Main Window

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Menus and Toolbars

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Protocol Task Bar

Quick access to subprotocols

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SciTegic Help Center

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Create sharable folder on

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Pipeline Pilot server

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Fundamentals of Pipeline Pilot

Running an Existing Protocol

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Creating a New Protocol

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Red components have one or more

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Reusing Component Information in Protocols

If multiple Pipe are

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Highlighting a component displays its parameter panel

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Component Help Text

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