Bioinformatic Resources: Difference between revisions
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===== Our Favorites ===== | ===== Our Favorites ===== | ||
[ | [https://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI BLAST] | ||
[ | [https://emboss.sourceforge.net/ EMBOSS] | ||
[ | [https://hmmer.org/ HMMER] | ||
[ | [https://www.ncbi.nlm.nih.gov/spidey/ SPIDEY] :mRNA to genomic alignment | ||
===== Multiple Alignment ===== | ===== Multiple Alignment ===== | ||
[ | [https://www.ebi.ac.uk/Tools/msa/clustalw2/ ClustalW2] | ||
[ | [https://www.tcoffee.org/ T_Coffee] | ||
[ | [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. | [https://echinodb.uncc.edu/ EchinoDB] :EchinoDB is a database consisting of amino acid sequence orthoclusters from 42 echinoderm transcriptomes. | ||
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===== Phylogenetic Analysis ===== | ===== 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. | ||
[ | [https://doua.prabi.fr/software/njplot NJplot tree drawing] | ||
===== Gene Prediction ===== | ===== Gene Prediction ===== | ||
[ | [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/ | ||
[ | [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 ===== | ||
[ | [https://bioinfo.ut.ee/primer3-0.4.0/ Primer 3, Release 1.0] | ||
[ | [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. | ||
[ | [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. | ||
[ | [https://www.tbi.univie.ac.at/RNA/ ViennaRNA] : RNA Secondary Structure Prediction and Comparison. | ||
[ | [https://www.repeatmasker.org/ RepeatMasker 3.2.8, with RepBase 20090604] | ||
===== Other Scientific Software ===== | ===== Other Scientific Software ===== | ||
Revision as of 12:47, 15 February 2023
Our Favorites
SPIDEY :mRNA to genomic alignment
Multiple Alignment
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.
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
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.