Is there any method to blast in other databases in blast2go program? help!?

[chadn737]

Here is the ftp site for the TAIR10 blast sets. You probably want one of the cds or cDNA files:

ftp://ftp.arabidopsis.org/home/tair/...R10_blastsets/

[hugh_hang]

The default configuration for online BLAST through the Blast2GO GUI application uses the NCBI QBlast service which provides only those databases listed; you can not add custom databases to this method.

Your alternatives to use different databases are:

1) Set up your own WWW-BLAST service (or find access to someone's who will share) which has or can be customized with the databases you want. Edit the blast2go.properties file on your local computer to designate this WWW-BLAST server as the default source for running your online BLAST searches through the Blast2GO GUI.

2) Run your BLAST search using a standalone (command line) BLAST installation against your custom database. Be sure to configure your BLAST search to output the results in XML format. Launch Blast2GO and load your FASTA sequence file as normal. From the File menu select "Import->Import Blast Results". Select your XML file (or files) for import. Once the BLAST results have been imported proceed with Mapping and Annotation as usual.

I recommend option #2 because it is easier and more scalable.

Thank you, I have thought of the option #2, but how can I get the database downloaded from TAIR in the format of .fasta with accession No. like AT4G22340

[kmcarr]

The default configuration for online BLAST through the Blast2GO GUI application uses the NCBI QBlast service which provides only those databases listed; you can not add custom databases to this method.

Your alternatives to use different databases are:

1) Set up your own WWW-BLAST service (or find access to someone's who will share) which has or can be customized with the databases you want. Edit the blast2go.properties file on your local computer to designate this WWW-BLAST server as the default source for running your online BLAST searches through the Blast2GO GUI.

2) Run your BLAST search using a standalone (command line) BLAST installation against your custom database. Be sure to configure your BLAST search to output the results in XML format. Launch Blast2GO and load your FASTA sequence file as normal. From the File menu select "Import->Import Blast Results". Select your XML file (or files) for import. Once the BLAST results have been imported proceed with Mapping and Annotation as usual.

I recommend option #2 because it is easier and more scalable.

[hugh_hang]

I have about 300 sequences to blast and analys with blast2go.
BUT, In blast2go, I can only blast several DBs in the option list, can i add another db (like TAIR) into it and run the blast2go? OR can some other applications both online or offline create a blast result which can be imported into blast2go?

Thanks a lot!