ARC Centre of Excellence for Plant Energy Biology

Pre-release edition

Rice DB imports Arabidopsis thaliana orthology clusters from InParanoid7.

Citations:

Ostlund G, Schmitt T, Forslund K, Kostler T, Messina DN, Roopra S, Frings O and Sonnhammer ELL. InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. Nucleic Acids Res. 38:D196-D203, 2009.

Usage When Searching Rice DB Usage Viewing Rice DB Results
  • You can search for Arabidopsis thaliana AGI-style At identifiers in InParanoid Rice orthology clusters.
  • Drop-down orthologous genes are available in summary results.
  • InParanoid cluster results can be shown in search results.
  • Rice loci can be joined side-by-side with orthologous genes via InParanoid.
  • Flat file info pages show orthology groups from InParanoid.
Example: show InParanoid, Affymetrix, summary for LOC_Os09g39670
Example: view InParanoid for LOC_Os02g06480.1, LOC_Os08g06060.1, Q5VQF5
Example: AT2G42960.1
Example: At5g58180.1
Example: find InParanoid orthology for LOC_Os01g64650.1
Example: find InParanoid orthology with At5g58180.1
Example: find InParanoid orthology for At5g58180.1
Example: At2g27150.1
Example: find InParanoid orthology for LOC_Os07g18120.1
Example: find InParanoid orthology with At2g27150.1
Example: find InParanoid orthology for LOC_Os01g04680.1
Example: find InParanoid orthology for LOC_Os01g35140.1
Example: find InParanoid orthology for At2g27150.1
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System Information

Transcript of last update

Took 8 seconds, 686 millis starting Thu, 19 Apr 2012 08:04:14 GMT:
Using /var/folders/75/983jwhw537q11ck7b_b0zwf80000gn/T/RiceDB/InParanoid_
Using db.local/downloaded/InParanoid_
Checking http://inparanoid.sbc.su.se/download/current/table_stats/InParanoid.A.thaliana-O.sativa

HTTP/1.1 200 OK
Date: Thu, 19 Apr 2012 08:04:15 GMT
Server: Apache/2.2.15 (CentOS)
Last-Modified: Wed, 29 Apr 2009 00:52:57 GMT
ETag: "4063c45-4c15f6-468a700144c40"
Accept-Ranges: bytes
Content-Length: 4986358
Content-Type: text/plain; charset=UTF-8
Connection: close

Importing header stats
Checking http://inparanoid.sbc.su.se/download/current/sqltables/sqltable.A.thaliana.fa-O.sativa.fa

HTTP/1.1 200 OK
Date: Thu, 19 Apr 2012 08:04:16 GMT
Server: Apache/2.2.15 (CentOS)
Last-Modified: Wed, 29 Apr 2009 00:52:57 GMT
ETag: "40628ee-16e24f-468a700144c40"
Accept-Ranges: bytes
Content-Length: 1499727
Content-Type: text/plain; charset=UTF-8
Connection: close

Importing TSV file
Making full text At index