Difference between revisions of "Family Alignment Documentation"

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(Introduction)
(Add apps)
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These pages describe approaches to characterizing sequence families in some set of related organisms. There are many ways to do this so our examples, though robust and proven by practice, are selected from a multitude of possible examples. The focus is on approaches that use a Bio* toolkit ([[http://www.biojava.org BioJava], [http://bioperl.org BioPerl], [http://biopython.org BioPython], [http://bioruby.org BioRuby]) since these packages offer the user different workflow possibilities but home-grown solutions are also discussed.
 
These pages describe approaches to characterizing sequence families in some set of related organisms. There are many ways to do this so our examples, though robust and proven by practice, are selected from a multitude of possible examples. The focus is on approaches that use a Bio* toolkit ([[http://www.biojava.org BioJava], [http://bioperl.org BioPerl], [http://biopython.org BioPython], [http://bioruby.org BioRuby]) since these packages offer the user different workflow possibilities but home-grown solutions are also discussed.
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All of our examples are descriptions of bioinformatic workflows or pipelines. A workflow is comprised of a set of analytical applications, performing the analyses themselves, and some set of scripts that hand data to applications and take results from these same applications. One will also frequently encounter some set of critical filters (e.g. in English, "only write those sequences to a file that match the query sequence with a p < .0001" or "get all nucleotide sequences > 250 bp in length from the input file"), and these filtering steps may be performed by an application or by a script.
  
 
===Analysis of Gene & Protein Families from Fungal Genomes===
 
===Analysis of Gene & Protein Families from Fungal Genomes===
  
 
Based on the work of Jason Stajich (http://fungal.genome.duke.edu/).
 
Based on the work of Jason Stajich (http://fungal.genome.duke.edu/).
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====Applications====
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* [http://selab.wustl.edu/cgi-bin/selab.pl?mode=software#trnascan tRNAscan]
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* [http://homepage.mac.com/iankorf/ SNAP]
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* [http://augustus.gobics.de/ AUGUSTUS]
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* [http://www.tigr.org/~salzberg/glimmer.html Glimmer]
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* [http://genes.mit.edu/GENSCANinfo.html Genscan]
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* [http://www.ncbi.nlm.nih.gov/BLAST/download.shtml BLASTZ]
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* [http://www.ncbi.nlm.nih.gov/BLAST/download.shtml BLASTN]
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* [http://www.ebi.ac.uk/~guy/exonerate/ exonerate]
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* [http://bioweb.pasteur.fr/docs/EMBOSS/est2genome.html protein2genome]
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* [http://bioweb.pasteur.fr/docs/EMBOSS/est2genome.html est2genome]
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====Databases====
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* [http://www.sanger.ac.uk/Software/Rfam/ RFam]
  
  
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Based on the work of Amy Bouck (http://visionlab.bio.unc.edu/).
 
Based on the work of Amy Bouck (http://visionlab.bio.unc.edu/).
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 +
====Applications====
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 +
* [http://www.ncbi.nlm.nih.gov/BLAST/download.shtml BLASTN]
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* [http://www.ncbi.nlm.nih.gov/BLAST/download.shtml BLASTX]
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* [http://www.ebi.ac.uk/research/cgg/tribe/ TribeMCL]
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* [http://www.igs.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html T_Coffee]
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* [http://www.ebi.ac.uk/Wise2/ Estwise]
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* [http://evolution.genetics.washington.edu/phylip.html Phylip]
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* [http://evolution.genetics.washington.edu/phylip/doc/retree.html Retree]
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* [http://abacus.gene.ucl.ac.uk/software/paml.html PAML]
  
  
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Based on the work of Stefanie Hartmann (http://visionlab.bio.unc.edu/).
 
Based on the work of Stefanie Hartmann (http://visionlab.bio.unc.edu/).
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 +
====Applications====
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* Software from O. Eulenstein
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* GeneTree
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* Mesquite
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* gtp
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* primetv & reconcile
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* softparsmap

Revision as of 13:59, 12 December 2006

Introduction

These pages describe approaches to characterizing sequence families in some set of related organisms. There are many ways to do this so our examples, though robust and proven by practice, are selected from a multitude of possible examples. The focus is on approaches that use a Bio* toolkit ([BioJava, BioPerl, BioPython, BioRuby) since these packages offer the user different workflow possibilities but home-grown solutions are also discussed.

All of our examples are descriptions of bioinformatic workflows or pipelines. A workflow is comprised of a set of analytical applications, performing the analyses themselves, and some set of scripts that hand data to applications and take results from these same applications. One will also frequently encounter some set of critical filters (e.g. in English, "only write those sequences to a file that match the query sequence with a p < .0001" or "get all nucleotide sequences > 250 bp in length from the input file"), and these filtering steps may be performed by an application or by a script.

Analysis of Gene & Protein Families from Fungal Genomes

Based on the work of Jason Stajich (http://fungal.genome.duke.edu/).

Applications

Databases


Analysis of Silent Substitutions Within a Genome or Across Multiple Genomes

Based on the work of Amy Bouck (http://visionlab.bio.unc.edu/).

Applications


Reconciling the Multiple Trees Created by Analyzing Genomes

Based on the work of Stefanie Hartmann (http://visionlab.bio.unc.edu/).

Applications

  • Software from O. Eulenstein
  • GeneTree
  • Mesquite
  • gtp
  • primetv & reconcile
  • softparsmap