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How to update ncbi-blast+?
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blastn command line
written by allifc •Hi - I'm new to bioinformatics and trying to use the command line version of blastn. The web version of blastn has an option to …
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Online and remote blastn producing different results
written by e •Using the following blastn command with the metameta_16S.amplicons.fasta file and the nt database located at /nfs1/CGRB/BlastDB/NCBI/latest_blast_DB/nt: ``` blastn -query metameta_16S.amplicons.fasta -task megablast -db /nfs1/CGRB/BlastDB/NCBI/latest_blast_DB/nt -out …
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Blast command line gives no hits
written by Vca80553 •Hi everyone, I am using the BLASTn program (command line) to analyze alignment of different nucleotide sequences against a custom database (containing around 450 fasta …
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Blastn command line tab format gives duplicates
written by elesbb91 •When using the tab output format, it causes multiple outputs of the same hit to show, but with different %identities and other attributes. When using …
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Cannot reproduce BLAST results returned by the WEB API on the shell-based BLAST+ 2.7.1
written by xerygi •I am trying to BLAST several sequences using the latest command line-based BLAST+ on a Linux machine. Whatever I do, I get the unfortunate "No …
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ncbi blast results in multi-sequence fasta file
written by a.rexI have a fasta file that has 1000s of sequences, i.e.: >loc.1 ATGGTTTTTCCGTATACTTCACTGACTGCTGCTTGTAATTTTTCAGCATCCTCAAATTTTCAATTGTCAGAAACATGTCTAAACAATGAGGTCCCTCCAGTATTTATAAATAGCAACGGCCAAAATTGTTCCCGGCCCAATATGTCTTATAATGCTGACTTTCAAGTTTCAAATAGTCATTGTAATGAAACCACTGACAGTATTGGTAGTGGTCAAAATACTACTACTGATATGAATTACGATCCAAATAATAGTCAGAACTTTTCATTTTCCTCAAATGTTCTTGGTAATCTACAAAACTGGAATGGTAAAAGATCTAATTATTTCAGTTACAAACTCAATGACATGAAACAATTTTATAATCAAGAAATACCGTTAGTGGACAATTCCGTACCGATTTACACAAATGG >loc.2 CAGGTAAAAATCTGGTTTCAAAATCGTCGGTCCAAGTATAAAAAGCTTATTAAGCAAGGTCAGGATCCAAGCATCCTGATGAATGGAGAATTTAATGACAGCATGGATGAAATGACGGAAGATCAAATCGACGAAGATAATTGTATCAAACCAAAAGCAGAAATGCTATTAACAAGCGATCCAAATAATCCTAGAGGCGATAGTTCTGATATTCCAACTGAAA I am using ncbi blastn in terminal against this file …
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BLAST: Trying to find parameters to get the same results via Python as via the NCBI BLAST web tool
written by tanny •I am running a nucleotide BLAST using Python/Biopython. However, I get less (67 hits) results than using the web BLAST (8660 hits) (blast.ncbi.nlm.nih.gov/Blast.cgi): https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=4EGEHGP901R Biopython …
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Blastn(Strand= Plus/Minus and Plus/Plus) explication
written by midoxHello, I posted my problem in another site but I have no answer. Maybe you can help me with my problem I used Blastn to …
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Blast Nucleotide Vs. Nucleotide, Plus-Minus Results Only
written by Burlappsack •<p>Hi Folks, <br/> I am interested in running a blastn search to search for complementary sequence (potential biological function) between two groups of sequences, (Query …