User:Wayne Decatur/Sequence analysis tools: Difference between revisions
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m adding some EMBOSS update stuff and a mac program |
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*[http://www.firstmarket.com/cutter/cut2.html old web cutter] | *[http://www.firstmarket.com/cutter/cut2.html old web cutter] | ||
*[http://www.protocol-online.org/tools/sms2/rest_map.html Sequence Manipulation Suite: Restriction Map - has at the left side links to other tools they have] | *[http://www.protocol-online.org/tools/sms2/rest_map.html Sequence Manipulation Suite: Restriction Map - has at the left side links to other tools they have] | ||
*[http://biotools.umassmed.edu/ Biotools | *[http://biotools.umassmed.edu/ Biotools at UMASS MED (formerly included EMBOSS] | ||
*[http://www.bioinformatics.nl/ `cons` alignment consensus program and many others at EMBOSS explorer website] | |||
*[http://emboss.sourceforge.net/ Links to many EMBOSS portals, servers and mirrors under 'Servers'] | |||
*[http://www.ebi.ac.uk/Tools/muscle/index.html MUSCLE: MUltiple Sequence Comparison by Log-Expectation] | *[http://www.ebi.ac.uk/Tools/muscle/index.html MUSCLE: MUltiple Sequence Comparison by Log-Expectation] | ||
*[http://www.phylosoft.org/archaeopteryx/ Archaeopteryx for the visualization of annotated phylogenetic trees.] | *[http://www.phylosoft.org/archaeopteryx/ Archaeopteryx for the visualization of annotated phylogenetic trees.] | ||
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* [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. | ||
* [http://www.t-profiler.org/index.html T-profiler] - for scoring the activity Of pre-defined groups of yeast genes using gene expression data **As of May 2016 it was not accepting uploads.** | * [http://www.t-profiler.org/index.html T-profiler] - for scoring the activity Of pre-defined groups of yeast genes using gene expression data **As of May 2016 it was not accepting uploads.** | ||
* [http://biit.cs.ut.ee/gprofiler/ g:Profiler] - for | * [http://biit.cs.ut.ee/gprofiler/ g:Profiler] - for characterizing and manipulating gene lists of high-throughput genomics. Handles yeast and many other organisms. | ||
* [http://biit.cs.ut.ee/gprofiler/ ProViz] - a web-based visualization tool to investigate the functional and evolutionary features of protein sequences. | * [http://biit.cs.ut.ee/gprofiler/ ProViz] - a web-based visualization tool to investigate the functional and evolutionary features of protein sequences. | ||
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* [http://skylign.org/ Skylign] | * [http://skylign.org/ Skylign] | ||
* [https://omarwagih.github.io/ggseqlogo/ Generating publication-ready sequence logos in R using ggseqlogo] | * [https://omarwagih.github.io/ggseqlogo/ Generating publication-ready sequence logos in R using ggseqlogo] | ||
== Installable software for fine-tuning sequence alignments== | |||
*[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4756450/#CR3 SEQOTRON] - Mac Software for adjusting sequence alignments by hand. Unfortunately it discards the conservation data if it is there in input. Haven't found a way to put it back in the output other than use [http://www.bioinformatics.nl/ `cons` alignment consensus program and many others at EMBOSS explorer website] | |||
==My own sequence work-related code== | ==My own sequence work-related code== | ||
