Originally posted by upendra_35
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Originally posted by hugh_hang View PostI've tried changing format but it doesn't work. I guess we should use TAIR10_pep... for BLAST DBs which is protein files.
A second thing to consider is do the IDs in you custom BLAST DB ('myid' in the example on the webpage) match IDs in the Blast2GO database. If the IDs don't match, Blast2GO won't be able to map them. Even if you reformatted the TAIR FASTA like the example in the tutorial and put the AT number in the proper position I'm not sure that TAIR AT numbers are in the Blast2GO database.
A workaround is to use this file from the TAIR site: At_GB_refseq_prot.gz. It is the same protein set but uses the NCBI RefSeq IDs and GI numbers for the IDs. For example:
Code:>gi|240256448|ref|NP_200529.4| PSD2 (phosphatidylserine decarboxylase 2); phosphatidylserine decarboxylase [Arabidopsis thaliana]
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Originally posted by kmcarr View PostBlast2GO is very particular about the format of the sequence ID used in FASTA files when you are creating custom BLAST databases. See this webpage for details about formatting your own BLAST DB for use with Blast2GO.
A second thing to consider is do the IDs in you custom BLAST DB ('myid' in the example on the webpage) match IDs in the Blast2GO database. If the IDs don't match, Blast2GO won't be able to map them. Even if you reformatted the TAIR FASTA like the example in the tutorial and put the AT number in the proper position I'm not sure that TAIR AT numbers are in the Blast2GO database.
A workaround is to use this file from the TAIR site: At_GB_refseq_prot.gz. It is the same protein set but uses the NCBI RefSeq IDs and GI numbers for the IDs. For example:
Code:>gi|240256448|ref|NP_200529.4| PSD2 (phosphatidylserine decarboxylase 2); phosphatidylserine decarboxylase [Arabidopsis thaliana]
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