User: arfaj a

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arfaj a10
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Posts by arfaj a

<prev • 35 results • page 1 of 4 • next >
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run fadiff to compare fasta files
... Hello, I want to extract the differences from two versions of one blast database. I am using php to do this task. first, i extract gi number only from each version using blastdbcmd. then, i do unix join that find the differences between the two gi files. then, i write while loop to read each gi fr ...
fasta ncbi blast written 3.6 years ago by arfaj a10
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Comparing two BLAST database files
... Hello, I develop an application to compare 2 blast database versions. I was using UNIX diff command for testing small text files and it was working great. This command finds the differences between text files. Now, I face issues when the text files are huge. Any suggested utility which can help me t ...
ncbi sequence blast-database blast written 3.7 years ago by arfaj a10 • updated 3.5 years ago by Biostar ♦♦ 20
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sequence gi number of updated sequences
... Hello, I have a question regarding sequence gi number. If I have 2 versions of blast database say OldDatabaseVersion and NewDatabaseVersion. The NewDatabaseVersion may have new sequences added, some sequences removed, or some sequences modified. If the sequence is removed from OldDatabaseVersio, ...
ncbi gi sequence blast written 3.7 years ago by arfaj a10 • updated 3.7 years ago by piet1.7k
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automate the running of update_blastdb.pl every week
... Hello all, Please, I want to schedule a task to run update_blastdb.pl every week. I can run it manually from cmd by typing: Perl update_blastdb.pl --passive --decompress refseq_rna It ran successfully. How can I schedule the task to run it automatically? and how can I pass the arguments: --passi ...
ncbi blast blastn written 3.7 years ago by arfaj a10
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Comment: C: failed to download blast db using update_blastdb.pl + decompress db file with up
... I actually have the latest version of blast+. It does not include the decompress in the update_blastdb.pl. Can I just replace the source code of update_blastdb.pl with the one have decompress option? is it save? ...
written 3.7 years ago by arfaj a10
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Comment: C: failed to download blast db using update_blastdb.pl + decompress db file with up
... Yes, I also see it in the source code on the ncbi site. The source code of my local update_blastdb.pl is different. Is it save to copy the content of update_blastdb.pl on the website to my local one? I really need to decompress. ...
written 3.7 years ago by arfaj a10
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Comment: C: failed to download blast db using update_blastdb.pl + decompress db file with up
... you are right. It does not mentioned in the documentation. But, I see it in different google search like: http://devbioinfo.to.cnr.it/doku.php?id=rachaelx:blastl ...
written 3.7 years ago by arfaj a10
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Comment: C: failed to download blast database using update_blastdb.pl
... Thanks, I think it from my connection. I have another question I will post it above. ...
written 3.7 years ago by arfaj a10
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failed to download blast db using update_blastdb.pl + decompress db file with update_blastdb.pl
... Hello all, **First,** I am trying to run update_blastdb.pl script to download updated database from ncbi ftp site but, got the following error in the command prompt: C:\inetpub\wwwroot\webclient\blast\bin>perl update_blastdb.pl refseq_rna Connected to NCBI Downloading refseq_rna (8 volumes) ... ...
ncbi update_blastdb.pl blast written 3.7 years ago by arfaj a10 • updated 3.7 years ago by Dr. Mabuse47k
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Comment: C: run BLASTn remotly
... So ? what can I do ? ...
written 3.7 years ago by arfaj a10

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