Bioops

Bioinformatics=(ACGAAG->AK)+(#!/bin/sh)+(P(A|B)=P(B|A)*P(A)/P(B))

Synteny Relevant Links

| Comments

Copy from http://www.symapdb.org/docs/links.html

Contents:

  • Information
  • On-line comparative sequenced genome databases
  • Synteny downloadable programs
  • A few multiple alignment programs

Information

Information Comments
Homology Wiki
Useful definitions Nature Reviews Genetics
Alignment software Wiki
Plant database USDA
Plant genomes GenBanks
Angliosperm Phylogeny Missouri Botanical Garden
Tree of Life Collaborative effort to provide information about biodiversity

On-line comparative sequenced genomes databases

Database Species;graphics;computation Publication
Phytozome Plants; Genome browsers; Hartmann et al. 2006
PLAZA Plants; Gene region alignments, Dotplot, Chromosome alignment, Multiplicon; blastp & OrthoMCL method Proost et al. 2009
Plant Genome Duplication Plants; Dotplots and detail; blastp & MCSCAN Tang et al. 2008
Gramene Grasses; Ensembl; Liang et al. 2008
Legume Information System Legumes; CMap;
JGI genome projects Various; Vista and links to Phytozome;
Vista Various; Java display of regions; Shuffle-LAGAN & BLAT in pipeline, allows user input. Frazer et al. 2004
Narcisse Various; Dotplots, circos, chromosome-based gene alignment; blastp & custom script. Courcelle et al. 2008
Cinteny Various; Genome/chromosome view; custom algorithm Sinha & Meller 2007
CoGe Various; Dotplot (SynMap) and ajax Genome Browser; DAGchainer, Blast Lyons & Freeling 2008
OrthoClusterDB No plants; Genome chromosome view, link to Gbrowse; OrthoCluster, allows user input. Ng et al. 2009
The Synteny Database No plants; Various views; Blastp & custom pipeline, emphasis on duplications and ohnologs. Catchen et al. 2009
Ensembl No plants; ComparaMart, DAS visualization; TreeBeST, Pecan. Hubbard et al. 2009
UCSC Genome Browser No plants; Miller et. al. 2007
Inparanoid Various, produce lists of orthologs Ostlund et al. 2009
OrthoMCL Various, produce lists of orthologs Li et al. 2003

Synteny Computation and/or Display Software

Key: Perfect - conserved order in block, Imperfect - allows micro-rearrangments in block, Duplications - allows duplicated regions, Multiplicon - mutually homologous segment between >2 genomes.
Software Input Synteny Graphics Publication
i-ADHoRe N gene lists Perfect, duplications, multiplicon Generates plots using Perl GD Vandepoele et al. 2002 Simmillion et al. 2007
AXTCHAIN BLASTZ alignments Kent et al. 2003
DiagHunter Similarity file Imperfect GenoPix Tcl/Tk Cannon et al. 2003
GRIMM-synteny Similarity file Imperfect, breakpoints Web Tessler 2002 andPevzner and Tessler 2003
FISH Ordered marker file per contig and pairs files Imperfect no Calabrese et al. 2003
DAGchainer Gene pairs with chromosome positions Perfect Dot plot Haas et al. 2004
ColinearScan Protein sequences with positions and pairs file Perfect, estimates gap parameters. no Wang et al. 2006
OSfinder Homologous markers with locations (provide scripts to generate this file from different sources) Perfect, estimates all parameters, no duplication PNG file of blocks and of dotplot Hachiya et al. 2009
OrthoCluster Imperfect Vergara & CHen 2009
Cyntenator guided tree & similarity files Conserved synteny between n genomes no Rodelsperger & Dieterich 2010
Mauve Multiple sequences (small genomes or regions) Conserved, aligns multiple sequences, computes synteny & breakpoints Java graphics & manager Darling et al. 2004
MCMuSeC Homologs for multiple genomes & phylogenetic tree Detects gene clusters no Ling et al. 2009
MCscan blast & gff file DAGchainer + consensus sequence builder no Tang et al. 2008
LineUp Genetic maps no Hampson et al. 2003
GenomeMatcher BLAST, MUMmer no Dotplots and closeup (seegallery) Ohtsubo et al. 2008
CMap Maps (genetic, FPC, sequence) no Perl/CGI (seescreen shots) Youens-Clark et al. 2009
GBrowse_syn Alignments no Perl/CGI GBrowse-based -
Circos GFF files no Perl/CGI Krzywinski et al. 2009

A few alignment programs

Software Input Computation Graphics Publications
Mummer Genome sequence Anchors Java graphical interface Kurtz et al. 2004
LAGAN Genome Sequence Vista Brudno et al. 2007
AVID Genome sequence Aligns and orders Vista Bray et al. 2003
Vista Alignments LAGAN or AVID Java (see screenshot) Frazer et al. 2004

Comments