User: navela78

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navela7850
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Posts by navela78

<prev • 21 results • page 1 of 3 • next >
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Comment: C: Taxonomy information in nr database
... Thanks for your suggestion. Your suggestion works for preformatted nr database downloaded from NCBI. However I need to make the nr database from scratch from the fasta file (because I need to add some information to sequence headers in the nr fasta file). My question is similar to this one https:/ ...
written 3 months ago by navela7850
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Taxonomy information in nr database
... How is taxonomy information injected into BLAST databases? My application logic is requiring me to rebuild nr from the fasta file (ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/) because I need to make some custom changes to the sequence headers: In that file the headers does not seem to have taxonom ...
nr blast written 3 months ago by navela7850 • updated 3 months ago by Istvan Albert ♦♦ 77k
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Comment: C: What are gene prediction methods with high sensitivity?
... If you don't care about false positive rate could you do 6 frame translations and find all ORFs? ...
written 3 months ago by navela7850
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Comment: C: Identifying database from which a hit sequence came from after blastdb_aliastool
... The databases are big but adding the db name in the headers seems to the only option right now. Thanks for your response. ...
written 3 months ago by navela7850
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Comment: C: Identifying database from which a hit sequence came from after blastdb_aliastool
... The blast result file contains "Database: custom_db" (i.e.) the alias in the beginning of the file and the end of the file. Is this what you meant by database identifier? There is no database identifier for each hit unless I am missing to set some blast option properly. ...
written 3 months ago by navela7850
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Identifying database from which a hit sequence came from after blastdb_aliastool
... I am using blastdb_aliastool to create custom databases (say custom_db = db1 + db2) to perform blast. Once I get blast results from custom_db is there a way to find which blast database (db1 or db2) a certain hit came from? ...
blast blastdb_aliastool written 3 months ago by navela7850 • updated 6 weeks ago by Biostar ♦♦ 20
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Comment: C: extract accessions from blastdbcmd
... Thanks genomax. Sorry for the miscommunication ... but i was looking to extract one accession per sequence for all sequences in nr. Looks like there is no blastdbcmd option for it ... so like you mentioned I created it on the fly like so: blastdbcmd -db nr -entry all -outfmt "%f" | awk '/>(. ...
written 3 months ago by navela7850
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Comment: C: extract accessions from blastdbcmd
... Thanks genomax. I just thought it will be easier to extract accessions this way than to write a script. Looks like there is no straight forward way in blastdbcmd to extract one accession per sequence? In that case I can work with the fasta file like you mentioned. My ultimate goal is to see how bla ...
written 3 months ago by navela7850
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extract accessions from blastdbcmd
... My copy of the nr database has about 148 million sequences which i found using blastdbcmd command using the -info option. However when I try to extract the accession numbers using the following command: blastdbcmd -db nr -entry all -outfmt "%a" I am getting much more than 148 million accessio ...
blastdbcmd blast written 3 months ago by navela7850 • updated 3 months ago by Biostar ♦♦ 20
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Comment: C: Technology Stack of NCBI (Genbank, GEO, etc.)
... Looks good! They don't explain genbank etc. in such detail. ...
written 4 months ago by navela7850

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