Bioinformatic Resources - Revision history

Ctelmer: /* Our Favorites */

2023-02-15T20:16:08Z

Our Favorites

← Older revision		Revision as of 20:16, 15 February 2023
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	[https://emboss.sourceforge.net/ EMBOSS]		[https://emboss.sourceforge.net/ EMBOSS]

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

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

Ctelmer: /* Our Favorites */

2023-02-15T19:58:39Z

Our Favorites

← Older revision		Revision as of 19:58, 15 February 2023
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	[https://emboss.sourceforge.net/ EMBOSS]		[https://emboss.sourceforge.net/ EMBOSS]

	~~[https~~://hmmer.org~~/ HMMER]~~		HMMER - http://hmmer.org

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

Ctelmer at 19:47, 15 February 2023

2023-02-15T19:47:46Z

Ctelmer at 00:13, 17 November 2022

2022-11-17T00:13:49Z

← Older revision		Revision as of 00:13, 17 November 2022
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	[http://doua.prabi.fr/software/seaview Seaview:alignment editor]		[http://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 =====

imported>Ctelmer: Ctelmer moved page Bioinformatic resources to Bioinformatic Resources: There was not a link to the Main Page.

2021-02-10T22:16:01Z

Ctelmer moved page Bioinformatic resources to Bioinformatic Resources: There was not a link to the Main Page.

← Older revision	Revision as of 22:16, 10 February 2021
(No difference)

imported>Echinobase: Created page with " ===== Our Favorites ===== [http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI BLAST] [http://emboss.sourceforge.net/ EMBOSS] [http://hmmer.org/ HMMER] [http://www.ncbi.nlm.nih..."

2020-02-12T21:37:58Z

Created page with " ===== Our Favorites ===== [http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI BLAST] [http://emboss.sourceforge.net/ EMBOSS] [http://hmmer.org/ HMMER] [http://www.ncbi.nlm.nih..."

New page

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

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

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

[http://hmmer.org/ HMMER]

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

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

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

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

[http://doua.prabi.fr/software/seaview Seaview:alignment editor]

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

[http://evolution.genetics.washington.edu/phylip.html 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.

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

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

[http://genes.mit.edu/GENSCAN.html 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

[https://ccb.jhu.edu/software/glimmerhmm/ 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/

[http://www.genezilla.org/ 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 =====

[http://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.

[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 
efficiently.

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

[http://www.repeatmasker.org/ 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.

← Older revision		Revision as of 19:47, 15 February 2023
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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]		[https://hmmer.org/ HMMER]

	[~~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.		[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 =====

	[~~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 />
Line 34:		Line 34:
	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 =====