Hi all!
I have generated genome assemblies for my samples and would like to find the location of coding sequences in the contigs. Using coding...
160 results in 0.0045 seconds.
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Command line BLAST to identify genes in genome assemblies
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blast nr database not working
So I am trying to download the latest nr database and use blast with it on Ubuntu 16.04. I compiled and installed the latest blast and then used update_blastdb.pl... -
Makeblastdb error: file does not exist.
I just downloaded the blast command line applications and I would like to make a database of a MGEs nucleutides that i downloaded from ACLAME database... -
Viral Genome reconstruction
Hi! I have some reads from sequencing a viral genome. We are analyzing readings with two matches, and we calculate the existing distance between both... -
Blastp DBv5 Entrez_query Problems
Hello anyone,
in the previous version of Blast DB it was possible to limit the search for blastp against the HMP (Human Microbiome Project)... -
[NEWBIE] [BLAST] Return of Non-Aligned Proteins
Hi, so, i'm working with some rvac project and i want to do something like this:
i have a protein aminoacid sequence and i run a blast... -
[NEWBIE] Interpretation of blastp results
I'm extremely new to this and I apologize if this question seems naive. I created a database for virulence factors and did BLASTP.
I got... -
Pfam search using hmmer but only for a specific taxonomy
I am trying to do a de novo assembly using Trinity. Using Transdecoder and blastp/hmmscan search to do annotation (using Uniprot/pfam databases). htt... -
Combining BLAST nt and local database
Hi all,
I've made a custom local BLAST database and I'm trying to 'combine' it with the BLAST nt database using ncbi-blast-2.9.0+ blastdb_aliastool... -
Combining BLAST nt and local database
Hi all,
I've made a custom local BLAST database and I'm trying to 'combine' it with the BLAST nt database using ncbi-blast-2.9.0+ blastdb_aliastool... -
Is it possible to print DNA sequences of subject organism in tblastn?
I did tblastn analysis by following command
...HTML Code:tblastn -query t3ss.fasta -subject org1.fasta -outfmt '6 qseqid qstart qend sseqid sstart send pident
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Error with makeblastdb from UniProt fasta file: no sequences were found
Hello there
I am trying to create a custom database for BLAST to run a local BLAST with some of my own proetin sequences.
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Protein annotation parameters (query or subject coverage?)
Hi there.
I am annotating some proteins' functions and I a have some doubts about the parameters I should use. I'm using e-value below... -
Getting (local) tBlastx working, error: Protein provided for nucleotide sequence
Any help would be much appreciated, I am trying to get tBlastx to work but not having any luck (error message and query in attached image).
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BLAST taxid to complete linage using biopython on a local machine.
Hello all,
Using BLAST, I am trying to identify thousands of sequences. To make my job a bit easier, I would like to classify these sequences...
