Escolar Documentos
Profissional Documentos
Cultura Documentos
SUBMITTED TO :
Mr. M.V.PARAKHIYA Asst. PROFESSOR, DEPT.OF BIOCHEMISTRY JAU, JUNAGADH.
SUBMITTED BY: SAHIL PATEL M.Sc.(PLANT BIOTECH) REGD. NO.:J4-00399-2008, DEPT. OF BIOCHEMISTRY, JAU, JUNAGADH.
INDEX
Introduction Types of Bioinformatics Software's
Bioinformatics
a definition ?
The design, construction and use of software tools to generate, store, annotate, access and analyse data and information relating to Molecular Biology
OR
Biologists doing stuff with computers?
Bioinformatics Software:
The Bioinformatics tools are the software programs for the saving, retrieving and analysis of Biological data and extracting
the information from them.
Sequence Databases
Bioinformatics Software's
BLAST
The Basic Local Alignment Search Tool (BLAST) for comparing gene and protein sequences against others in public databases There are several types including PSI-BLAST, PHIBLAST, and BLAST 2 sequences. Specialized BLASTs are also available for human, microbial, malaria, and other genomes, as well as for vector contamination, immunoglobulins, and tentative human consensus sequences.
Types of BLAST
Nucleotide BLAST : Search a nucleotide database using a nucleotide query Protein BLAST : Search protein database using a protein query BLASTx : Search protein database using a translated nucleotide query tBLASTn : Search translated nucleotide database using a protein query tBLASTx : Search translated nucleotide database using a translated nucleotide query
Applications of BLAST
Make specific primers with Primer-BLAST
Applications of BLAST
Search immunoglobulins (IgBLAST) Search for SNPs (snp)
FASTA
A database search tool used to compare a nucleotide or peptide sequence to a sequence database.
The program is based on the rapid sequence algorithm described by Lipman and Pearson.
EMBOSS
EMBOSS (The European Molecular Biology Open Software Suite) is a new, free open source software analysis package specially developed for the needs of the molecular biology user community. Within EMBOSS there are around 100 programs (applications) for sequence alignment, database searching with sequence patterns, protein motif identification and domain analysis, nucleotide sequence pattern analysis, codon usage analysis for small genomes, and much more.
ClustalW
ClustalW is a general purpose multiple sequence alignment program for DNA or proteins.
It produces biologically meaningful multiple sequence alignments of divergent sequences, calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen.
RasMol
It is a powerful research tool to display the structure of DNA, proteins, and smaller molecules. Protein Explorer, a derivative of RasMol, is an easier to use program.
SWISS-PROT
This Database is maintained by Swiss Institute of Bioinformatics(SIB) and EMBL. SWISS-PROT provides a high level of annotation , a minimum level of redundancy and high level of integration with other database.
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Software Tools
General Packages: Packages that offer a comprehensive range of bioinformatics tools for sequence analysis. Most researchers would expect to use such packages at some time.
Specialised Packages
Packages that offer tools for a particular type of analysis. Used intensely by researchers in the relevant area, not at all by everyone else.
WWW Resources
Tools whose nature inclines them to be primarily accessed over the network.
General Packages:
GCG Wisconsin Package
Commercial
WWW and X GUIs Widely available
UNIX only
Comprehensive
Open source Several GUIs (java, WWW, X) Similar structure to the GCG package
Windows, MacOS X, UNIX Open source Excellent GUI including interactive graphical output Not comprehensive but allows access to EMBOSS
General Packages:
Commercial
Expensive
Other options
Windows PCs or Macintoshes Good GUIs
Public Domain
Free academic licence Excellent base call confidence estimation (phred) Excellent large scale contig assembler (phrap) Available by anonymous ftp
Excellent GUI
Excellent contig editor Excellent finishing tools Simple confidence estimation Contig assembler not good for big projects BUT phred and phrap can be accessed from Staden GUI
Insight II
PHYLIP
Incorporated into the EMBOSS general package
Commercial, but reasonable UNIX, VMS, DOS and windows Incorporated into the GCG general package
Most general packages include tools to access local sequence databases EMBOSS programs can access sequences from remote SRS servers
WWW Resources
Very popular, very widely available Not sensitive But extremely fast
FASTA
WWW Resources
Fully sensitive
MPsrch
Burkhard Rost
Both JPred and PHD work best from aligned protein families Simpler methods predicting from single sequences in most general packages
Expasy
Gene finding
Primer design
primer3 at the MIT (Available by anonymous ftp) Primer design in most general packages Primer design in EMBOSS is primer3
Sequence Databases Contain both raw sequence data and annotation DNA Sequences (European Molecular Biology Laboratory)
GenBank (NCBI)
DNA Data Bank of Japan
Refseq (NCBI)
Alignments and Patterns Alignments Aligned protein families Comprised of a number of sections
Alignments and Patterns Patterns Patterns are largely derived from the conserved portions of aligned protein families Representations of single motifs
Database are available from WWW sites and highly interlinked OMIM MGMD Clinical and Mutation
Bibliographic
PubMed
PDB
Integrated
Ensembl
Application Programs
JAVA in Bioinformatics Due to Platform independence nature of Java, it is emerging as a key player in bioinformatics. Perl in Bioinformatics Perl is also being used in the processing of biological data.
Thank You