Bioinformatics Resources (compiled by Dr. Qiang Tu)

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NCBI BLAST

EMBOSS

HMMER

SPIDEY :mRNA to genomic alignment

Multiple Alignment

ClustalW2

T_Coffee

Seaview:alignment editor

Phylogenetic Analysis

Phylip 3.66:phylogenetic analysis

  • Note: be sure to install libxaw7 and dev dbg headers packages before
    compile 3.66;
  • Note: This package is compiled from the latest version, not the EMBOSS
    integrated phylip 3.6, which can be done by './configure --prefix=/usr/local'; not debian phylip 3.6.1.

Molphy 2.3b: Maximum Likelihood.

Tree-Puzzle 5.2: Maximum Likelihood.

NJplot tree drawing

Gene Prediction

GENSCAN
Note: The document can be found in /usr/local/share/genescan. Three trained models are available: HumanIso.smat, Arabidopsis.smat, Maize.smat.My personal experience is that Humalso is much better than other two for sea urchin.example: genscan /usr/local/share/genscan/HumanIso.smat mycontig.fasta

GlimmerHMM, 2.0.4
Note: The document can be found in /usr/local/share/GlimmerHMM. Two trained models are available: arabidopsis and rice. Not good for sea urchin. But user can train their own model. example: glimmerhmm
Contig600303.fasta –d /usr/local/share/GlimmerHMM/trained_dir/arabidopsis/

GeneZilla, 1.0, former TigerScan
Note: Only one model trained for human available now(/usr/local/share/genezilla). User has to go genezilla directory to run the program. example: ./genezilla human.iso ~/mycontig.fasta

Other bioinformatics software

Primer 3, Release 1.0

Artemis 7:a DNA sequence viewer and annotation tool. Use 'art' to launch the artemis; use 'act' to launch ACT, a DNA sequence comparison viewer.

CD-HIT, v3.0.2(2006-0411) :CD-HI/CD-HIT clusters protein sequence database at high sequence identity threshold. This program can remove the high sequence redundancy
efficiently.

ViennaRNA : RNA Secondary Structure Prediction and Comparison.

RepeatMasker 3.2.8, with RepBase 20090604

Other Scientific Software
  • R 2.9
  • Gnuplot 4.2
  • Grace 5.1.22
Programming Resources
  • Python 2.3.5, BioPython 1.41
  • Perl 5.8, BioPerl 1.4
  • GCC 4.0.3
  • J2SE 1.5