Software Tools

Matlab Bioinformatics Toolbox

Software Tools for Sequence Analysis:

  • AceDB – a tool for viewing and managing genomic data
  • Artemis / ACT – Artemis: genome viewer and annotation tool, and ACT: (Artemis Comparison Tool) a DNA sequence comparison viewer based on Artemis
  • BLAST – Basic Local Alignment Search Tool for sequence similarity searching against nucleotide and protein databases
  • bl2seq – compare two sequences using BLAST (both sequences either protein or nucleotide)
  • ClustalW – multiple sequence alignment program for DNA/proteins. Graphic interface, ClustalX, also available
  • EMBOSS – a suite of around 100 bioinformatics tools
  • FASTA – Sequence similarity searching against nucleotide and protein databases
  • formatdb – Prepare a nucleotide or protein sequence file for seaching using BLAST
  • Glimmer – (Gene Locator and Interpolated Markov Modeler) a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.
  • GENSCAN – predicts the locations and exon-intron structures of genes in genomic DNA
  • Jalview – a multiple sequence alignment editor written in java
  • MSPcrunch – a BLAST output filtering tool
  • MUMmer – a system for rapidly aligning entire genomes
  • OligoArray – computes gene specific oligonucleotides for genome-scale oligonucleotide microarray construction
  • Phred, Phrap and Consed – Phred: reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base; Phrap: assembles shotgun DNA sequence data using the base calls and base quality values produced by Phred; Consed: a tool for viewing, editing, and finishing sequence assemblies created with Phrap
  • Primer3 – design primers within a DNA sequence
  • RepeatMasker – screens DNA sequences for interspersed repeats and low complexity DNA sequences
  • Readseq – reads sequence files and interconverts between many different sequence file formats
  • sim4 – aligns an expressed DNA sequence (EST, cDNA, mRNA) with a genomic sequence for the gene
  • SRS – (Sequence Retieval System) for database and cross-database querying
  • Staden – a set of DNA sequence assembly, editing and analysis tools
  • STARS – an alternative interface to Staden for sequence assembly of sequence typing projects
    – External link:
  • T-COFFEE – a DNA or protein multiple sequence alignment package
    – External link: