Tools for Bioinformatics

Bioinformatic tools installed (Updating…)

Bioinformatic is a fast growing field of research. There are thousands of Bioinformatic software in the world, and most of them are free!

Here are only some examples for the most commonly used software installed on the server. If needed, we can install any available software on the server, and custom installation is allowed for registered users.

BLAST Tools

  1. ncbi-blast (including blastn, blastp, tblastn, blastx, tblastx): the most widely used sequence similarity search tool
  2. psi-blast: Position-Specific Iterated BLAST
  3. phi-Blast: Pattern-Hit Initiated BLAST
  4. mpiBLAST: BLAST search by parallel computing

Alignment tools

  1. Clustalw2: the most widely used multiple sequence alignment tool
  2. Clustalw-mpi:   multiple sequence alignments by parallel computing
  3. BaliScore: Scoring multiple sequence alignments
  4. MAFFT:   a multiple sequence alignment tool
  5. MUSSLE:   a multiple sequence alignment tool
  6. TCoffee: a multiple sequence alignment tool
  7. CAUSA: Codon-AA  Unified Sequence Alignment, a coding DNA sequence multiple sequence alignment tool developed by our team.

RNA

  1. QRNA: a non-coding RNA prediction tool
  2. microTar and microTar-mpi: a microRNA target prediction tool based on mRNA sequence complementarity (3′-UTR seed matches) and RNA duplex energy prediction, assessing the impact of microRNA binding on complete mRNA molecules.

Genome assembler

  1. Velvet
  2. ABySS
  3. SoapDenovo
  4. PANDASeq

Comparative genomics

  1. VISTA http://genome.lbl.gov/vista/index.shtml
  2. ACT http://www.webact.org/WebACT/home
  3. MUMMER http://mummer.sourceforge.net/
  4. MAUVE http://darlinglab.org/mauve/mauve.html

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