1. AB- BLAST
- This software package is used for gene and protein identification by applying the similarity searches of protein and nucleotide sequence databases.
- http://www.advbiocomp.com/blast.html
- The world’s largest antibody manufacturer by taking genomic/ proteomic approach for the antibody development which is in contrast with the traditional method of antibody production.
- http://www.abnova.com/
3. NCBI BLAST
- BLAST finds regions of local similarity between sequence.
- Compares nucleotides or proteins sequences to sequence databases and calculates the statistical significance of matches.
- Infer functional and evolutionary relationships between sequences as well as help to identify members of gene families.
- http://blast.ncbi.nlm.nih.gov/
- A collection of 3530 Pathway/ Genome databases.
- Provide tools for navigating, visualizing, and analyzing the underlying databases, and for analyzing omics data.
- http://www.biocyc.org/
5. Biolayout
- Biolayout Express 3D is designed for visualisation of huge graphs in two and three dimensional space derived from biological data.
- It is also used in the clustering, exploring and analyzing large sized graphs in two and three dimensional space derived from biological data.
- http://www.biolayout.org/
6. Bioruby
- Bioruby is equipped with a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, especially for the Ruby programming language.
- It consists of different components for the analysis of sequence, analysis of pathway, protein modelling and analysis of phylogenetic.
- http://www.bioruby.org/
7. Biosearch-2D
- BioSearch-2D renders the contents of large biomedical document collections into a single, dynamic map.
- With this, users can generate a summary map of genes versus ontology topics that match those provided by expert human reviewed articles.
- It also provides users a context specific, functtional annotation system for high-throughput gene signatures and ad-hoc gene lists.
- http://portal.ncibi.org/gateway/biosearch2d.html
8. Bowtie
- Bowtie is an ultrafast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences to large genomes.
- It aligns 35 base-pair reads to the human genome at a rate of 25 million reads per hour on a typical workstation.
- It also indexes the genome with a Burrows Wheeler index to keep its memory footprint small.
- http://bowtie-bio.sourceforge.net/index.shtml
9. BWA
- BWA is used for mapping low-divergent sequences against a large reference genome, for instance human genome.
- It comprises three algorithms such as BWA-backtrack, BWA-SW amd BWA-MEM.
- http://bio-bwa.sourceforge.net/bwa.shtml
10. Clustal Omega
- Clustal Omega is a new multiple sequence alignment program.
- It uses seeded guide trees and HMM profile-profile techniques to generate alignments.
- http://www.ebi.ac.uk/Tools/msa/clustalo/
11. Cross_Match
- Cross_Match is used for comparing any two DNA sequence sets using a 'banded' version of swat.
- Swat is a program for searching one or more DNA or protein query sequences, or a query profile, against a sequence database, using an efficient implementation of the Smith-waterman or Needleman-Wunsch algorithms with linear gap penalties.
- http://www.phrap.org/phredphrapconsed.html
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