Bioinformatics Software's

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.

DEPARTMENT OF BIOCHEMISTRY, JAU, JUNAGADH.

INDEX
Introduction Types of Bioinformatics Software's

Bioinformatics Software's Useful Programs in Bioinformatics

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.

Types of bioinformatics software's

Sequence Databases

Pathway Analysis Tools

Structure Prediction and Analysis Tools Sequence Analysis Tools

Sequence Management Tools

Visualization Tools

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

Search trace archives

Find conserved domains in your sequence (cds) Find sequences with similar conserved domain architecture (cdart) Search sequences that have gene expression profiles (GEO)

Applications of BLAST
Search immunoglobulins (IgBLAST) Search for SNPs (snp)

Screen sequence for vector contamination

Align two sequences using BLAST (bl2seq) Search protein or nucleotide targets in PubChem BioAssay

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.

These categorisations are very general

Many specialist programs are incorporated into the general packages.

Most things can be done at a web site somewhere.

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

UNIX only Comprehensive

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

Windows, Macintosh, UNIX

Modern intuitive GUI

Access remote databases

Specialised Packages Sequencing Project Management

The Phred - Phrap Package By Phil Green et al

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

Specialised Packages DNA/RNA Folding

Free for academic use Can be installed locally or run via a WWW page Incorporated into the GCG general package

Michael Zuker`s Programs

Protein Structure Analysis

Nominal fee for academic use LINUX, IRIX, Windows

Whatif by Gert Vriend

Specialised Packages Protein Structure Analysis for very rich people

SYBYL IRIX, HP-UX, LINUX

Insight II

IRIX, AIX, LINUX

Both systems are very impressive @ very expensive

Specialised Packages Phylogeny

Available by anonymous ftp Windows, Macintosh, UNIX

PHYLIP
Incorporated into the EMBOSS general package

Commercial, but reasonable UNIX, VMS, DOS and windows Incorporated into the GCG general package

WWW Resources Database Retrieval

Sequence Retrieval System

Retrieves MUCH more than sequences

Core elements free to academic sites Bioscience AG Implemented in many places

It is possible to integrate analysis tools

Elements of SRS are incorporated into EMBOSS

WWW Resources Database Retrieval

Retrieves MUCH more than sequences

Access to NCBI databases only

Entrez client software available by anonymous ftp

Most general packages include tools to access local sequence databases EMBOSS programs can access sequences from remote SRS servers

Database Similarity Searching

WWW Resources

Very popular, very widely available Not sensitive But extremely fast

FASTA

Popular, widely available Not sensitive much slower than blast

Can be installed locally or run via a WWW page

BOTH blast & fasta

Available by anonymous ftp (blast, fasta)

DNA/Protein query V DNA/Protein database

Incorporated into the GCG general package

Database Similarity Searching

WWW Resources

Fully sensitive

Slow algorithm fast computers

MPsrch

Protein V Protein only

Major use when blast/fasta fail

Exclusively a WWW resource

WWW Resources Structure prediction

Was consensus service now JNet only

JNet available by anonymous ftp

Older service, similar approach to JNet

Burkhard Rost

Main element is called PHD

Both JPred and PHD work best from aligned protein families Simpler methods predicting from single sequences in most general packages

WWW Resources Other WWW services

General Services: EBI And many more Pasteur Institute

Protein sequence analysis

Expasy

Gene finding

genscan at the MIT

(Free academic license)

Simple gene finding in most general packages

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)

Protein Sequences Refseq (NCBI) PIR Trembl (GenPept)

Alignments and Patterns Alignments Aligned protein families Comprised of a number of sections

Aligned protein domains

Automatically generated from protein sequence databases

Conserved blocks of protein alignments

Used to compute scoring schemes for protein comparisons

Alignments and Patterns Patterns Patterns are largely derived from the conserved portions of aligned protein families Representations of single motifs

Now comprised of both simple patterns and HMM profiles

Representations of patterns of motifs (fingerPRINTS)

Database are available from WWW sites and highly interlinked OMIM MGMD Clinical and Mutation

Bibliographic

PubMed

Raw Sequence Alignments and Patterns Structural

As accessed for sequence retrieval

As generated by analysis software

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