Copy from http://www.symapdb.org/docs/links.html
>>>>>>> d80cd8fa3e1fb5461144707ba04f7385ec6726a7:2011/02/synteny-relevant-links/index.html
Contents:
- Information
- On-line comparative sequenced genome databases
- Synteny downloadable programs
- A few multiple alignment programs
Information
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
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