User:Wayne Decatur/Sequence analysis tools: Difference between revisions
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* [http://www.premierbiosoft.com/netprimer/ Netprimer] | * [http://www.premierbiosoft.com/netprimer/ Netprimer] | ||
*[http://www.dyogen.ens.fr/genomicus-60.01/cgi-bin/search.pl Genomicus: Genomes in Evolution - "genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologically along evolutionary time." ] | *[http://www.dyogen.ens.fr/genomicus-60.01/cgi-bin/search.pl Genomicus: Genomes in Evolution - "genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologically along evolutionary time." ] | ||
*[https://code.google.com/p/seqtrace/ SeqTrace]- "is an application for viewing and processing DNA sequencing chromatograms (trace files). SeqTrace makes it easy to quickly generate high-quality finished sequences from a large number of trace files. SeqTrace can automatically identify, align, and compute <nowiki>[</nowiki>contig<nowiki>]</nowiki> consensus sequences from matching forward and reverse traces, filter low-quality base calls, and perform end trimming of finished sequences. The finished DNA sequences can then be exported to common sequence file formats, such as FASTA. " Written in Python. | *[https://code.google.com/p/seqtrace/ SeqTrace]- "is an application for viewing and processing DNA sequencing chromatograms (trace files). SeqTrace makes it easy to quickly generate high-quality finished sequences from a large number of trace files. SeqTrace can automatically identify, align, and compute <nowiki>[</nowiki>contig<nowiki>]</nowiki> consensus sequences from matching forward and reverse traces, filter low-quality base calls, and perform end trimming of finished sequences. The finished DNA sequences can then be exported to common sequence file formats, such as FASTA. " Written in Python. | ||
*[http://doua.prabi.fr/software/cap3 CAP3 Sequence Assembly Program] - online, webserver for making contigs from DNA sequences. "form allows you to assemble a set of contiguous sequences (contigs) with the CAP3 program. | *[http://doua.prabi.fr/software/cap3 CAP3 Sequence Assembly Program] - online, webserver for making contigs from DNA sequences. "form allows you to assemble a set of contiguous sequences (contigs) with the CAP3 program. | ||
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*[http://pax-db.org/#!home PaxDb]: Protein Abundance Across Organisms | *[http://pax-db.org/#!home PaxDb]: Protein Abundance Across Organisms | ||
* [https://bhapp.c2b2.columbia.edu/PrePPI/ PrePPI]: database of predicted and experimentally determined protein-protein interactions (PPIs) for yeast and human. | * [https://bhapp.c2b2.columbia.edu/PrePPI/ PrePPI]: database of predicted and experimentally determined protein-protein interactions (PPIs) for yeast and human. | ||
==Converters== | ==Converters== | ||
* [http://sing.ei.uvigo.es/ALTER/ ALTER (ALignment Transformation EnviRonment)] - complex interface but offers lots of options for output. I used it as part of my workflow to get closer to special NEXUS format (or intermediate) for performing maximum likelihood phylogenetic analysis of large sets of sequences. | * [http://sing.ei.uvigo.es/ALTER/ ALTER (ALignment Transformation EnviRonment)] - complex interface but offers lots of options for output. I used it as part of my workflow to get closer to special NEXUS format (or intermediate) for performing maximum likelihood phylogenetic analysis of large sets of sequences. | ||
* [http://sequenceconversion.bugaco.com/converter/biology/sequences/clustal_to_fasta.php Sequence conversion Provided by bugaco.com] - a lot of conversion choices with easy interface. When I had interleaved clustal format it converted nicely to a straight fasta listing for the sequence for every organism. | * [http://sequenceconversion.bugaco.com/converter/biology/sequences/clustal_to_fasta.php Sequence conversion Provided by bugaco.com] - a lot of conversion choices with easy interface. When I had interleaved clustal format it converted nicely to a straight fasta listing for the sequence for every organism. | ||
==Random sequence generators== | ==Random sequence generators== | ||
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* http://www.faculty.ucr.edu/~mmaduro/random.htm | * http://www.faculty.ucr.edu/~mmaduro/random.htm | ||
* http://molbiol.ru/eng/scripts/01_16.html | * http://molbiol.ru/eng/scripts/01_16.html | ||
==Sequence shufflers== | ==Sequence shufflers== | ||
* http://emboss.sourceforge.net/ - shuffleseq from EMBOSS shuffles a set of sequences maintaining composition. | * http://emboss.sourceforge.net/ - shuffleseq from EMBOSS shuffles a set of sequences maintaining composition. | ||
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==NGS== | ==NGS== | ||
* [http://homer.salk.edu/homer/basicTutorial/genomeBrowsers.html HOMER] - "Software for motif discovery and next-gen sequencing analysis". Nice in that it actually explains some of the details and advantages of the browsers and file types. | * [http://homer.salk.edu/homer/basicTutorial/genomeBrowsers.html HOMER] - "Software for motif discovery and next-gen sequencing analysis". Nice in that it actually explains some of the details and advantages of the browsers and file types. | ||
==Nucleic acid system building== | ==Nucleic acid system building== | ||
* [http://www.nupack.org/ NUPACK] - "NUPACK is a growing software suite for the analysis and design of nucleic acid systems." | * [http://www.nupack.org/ NUPACK] - "NUPACK is a growing software suite for the analysis and design of nucleic acid systems." | ||
