User: navela78

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navela7860
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Posts by navela78

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Comment: C: num_threads with blastn in blast 2.6.0+
... have you tried it and seen it using multiple cores? ...
written 17 months ago by navela7860
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num_threads with blastn in blast 2.6.0+
... Can someone confirm that using the -num_threads option uses multiple cores for blastn in blast2.6.0+? I am unable to get blastn running on multiple cores even for part of the blast process. I am blasting against the nt database. blastp against nr database uses multiple cores when num_threads is se ...
blast written 17 months ago by navela7860
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what is vdb_names in blastdb_aliastool
... Like the title says what does any one know what is vdb_names? what is VDB? Just trying to understand .... ...
blast written 17 months ago by navela7860 • updated 17 months ago by h.mon29k
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making nr database using makeblastdb
... Hello, I am creating a local nr blast database using the following command makeblastdb -parse_seqids -dbtype 'prot' -in nr.fa -out nr -title nr -hash_index it creates files like: nr.00.phd nr.00.phr nr.00.pog nr.00.psi nr.00.phi nr.00.pin nr.00.psd nr.00.psq However, the files here f ...
nr blast written 17 months ago by navela7860
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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 2.1 years ago by navela7860
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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 2.2 years ago by navela7860 • updated 2.2 years ago by Istvan Albert ♦♦ 84k
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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 2.2 years ago by navela7860
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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 2.2 years ago by navela7860
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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 2.2 years ago by navela7860
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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 2.2 years ago by navela7860 • updated 2.0 years ago by Biostar ♦♦ 20

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