Bioinformatic Resources: Difference between revisions

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===== Our Favorites =====
===== Our Favorites =====


[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI BLAST]
[https://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI BLAST]


[http://emboss.sourceforge.net/ EMBOSS]
[https://emboss.sourceforge.net/ EMBOSS]


[http://hmmer.org/ HMMER]
HMMER - <nowiki>http://hmmer.org</nowiki>


[http://www.ncbi.nlm.nih.gov/spidey/ SPIDEY] :mRNA to genomic alignment
[https://www.ncbi.nlm.nih.gov/spidey/ SPIDEY] :mRNA to genomic alignment


===== Multiple Alignment =====
===== Multiple Alignment =====


[http://www.ebi.ac.uk/Tools/msa/clustalw2/ ClustalW2]
[https://www.ebi.ac.uk/Tools/msa/clustalw2/ ClustalW2]


[http://www.tcoffee.org/ T_Coffee]
[https://www.tcoffee.org/ T_Coffee]


[http://doua.prabi.fr/software/seaview Seaview:alignment editor]
[https://doua.prabi.fr/software/seaview Seaview:alignment editor]
 
[https://echinodb.uncc.edu/ EchinoDB] :EchinoDB is a database consisting of amino acid sequence orthoclusters from 42 echinoderm transcriptomes.


===== Phylogenetic Analysis =====
===== Phylogenetic Analysis =====


[http://evolution.genetics.washington.edu/phylip.html Phylip 3.66:phylogenetic analysis]
[https://evolution.genetics.washington.edu/phylip.html Phylip 3.66:phylogenetic analysis]


* Note: be sure to install libxaw7 and dev dbg headers packages before<br />
* Note: be sure to install libxaw7 and dev dbg headers packages before<br />
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Tree-Puzzle 5.2: Maximum Likelihood.
Tree-Puzzle 5.2: Maximum Likelihood.


[http://doua.prabi.fr/software/njplot NJplot tree drawing]
[https://doua.prabi.fr/software/njplot NJplot tree drawing]


===== Gene Prediction =====
===== Gene Prediction =====


[http://genes.mit.edu/GENSCAN.html GENSCAN]<br />
[https://genes.mit.edu/GENSCAN.html GENSCAN]<br />
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
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


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Contig600303.fasta –d /usr/local/share/GlimmerHMM/trained_dir/arabidopsis/
Contig600303.fasta –d /usr/local/share/GlimmerHMM/trained_dir/arabidopsis/


[http://www.genezilla.org/ GeneZilla, 1.0, former TigerScan]<br />
[https://www.genezilla.org/ GeneZilla, 1.0, former TigerScan]<br />
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
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 =====
===== Other bioinformatics software =====


[http://bioinfo.ut.ee/primer3-0.4.0/ Primer 3, Release 1.0]
[https://bioinfo.ut.ee/primer3-0.4.0/ Primer 3, Release 1.0]


[http://www.sanger.ac.uk/science/tools/artemis 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.
[https://www.sanger.ac.uk/science/tools/artemis 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.


[http://bioinformatics.org/cd-hit/ 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<br />
[https://bioinformatics.org/cd-hit/ 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<br />
efficiently.
efficiently.


[http://www.tbi.univie.ac.at/RNA/ ViennaRNA] : RNA Secondary Structure Prediction and Comparison.
[https://www.tbi.univie.ac.at/RNA/ ViennaRNA] : RNA Secondary Structure Prediction and Comparison.


[http://www.repeatmasker.org/ RepeatMasker 3.2.8, with RepBase 20090604]
[https://www.repeatmasker.org/ RepeatMasker 3.2.8, with RepBase 20090604]


===== Other Scientific Software =====
===== Other Scientific Software =====

Latest revision as of 13:16, 15 February 2023


Our Favorites

NCBI BLAST

EMBOSS

HMMER - http://hmmer.org

SPIDEY :mRNA to genomic alignment

Multiple Alignment

ClustalW2

T_Coffee

Seaview:alignment editor

EchinoDB :EchinoDB is a database consisting of amino acid sequence orthoclusters from 42 echinoderm transcriptomes.

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 5.16, BioPerl 1.4
  • GCC 4.0.3
  • J2SE 1.5


Credit: Original list compiled by Dr. Qiang Tu
Note: This page has been flagged as requiring an update as some software versions are now out of date.