Downloading And Maintaining A Local, Blast-Able Nr Database
I am planning to set up and maintain a local version of the NR and other NCBI databases, for running in-house BLAST searches. I would also like to my local version of the databases be in synch with...
View ArticleNcbi Legacy Blast Usage With Tblastn/Pssm
I'm trying to get a webservice for protein discovery running. I would like to perform a tblastn with a PSSM from NCBI's archive (smp file). This works fine with NCBI BLAST+, but unfortunately the...
View ArticleCan I Have Blast Return One Hit Per Species
Hello all, I've been long troubled with redundant blast hits from different strains of the same species, for example, E. coli. These hits (can be dozens to hundreds) mask hits from other species which...
View ArticleQuality Analysis Of Pacbio Data
Hey GuysJust wondering if you guys have come across or developed any process to check for contamination in PacBio reads. By contamination what I mean is to align/blast the PacBio reads to some...
View ArticleBlastn - Program Runs Indefinitely When Generating Xml Formatted Output
I am running blastn on some nucleotide data, and it seems to run indefinitely when I generate XML output. The jobs take ~15 minutes when generating either the default format or tab delimited, but when...
View ArticleProblem With Interpretation Blast Results
Hi, I'm struggling with BLAST. I'm not sure if I can properly interpret the results of BLAST. Can anyone tell me when I can be sure that the sequences of the proteins are enough similar to be...
View ArticleIs there a good service for annotating transcripts?
After getting say 100k transcripts from an rna-seq project, generally one wants to annotate them against a database like nr, using say blastx. Problem is, this is very slow, taking e.g. a week with 24...
View ArticleStandalone Blast 2 Short Sequences
Hi. I'm new to blast. I have downloaded blast+ and installed on a windows machine. I want to use blast to align short nucleotide sequences (<400 bases) A against reads of similar length B. Set A and...
View ArticleBlast Can'T Find Databases
I've installed BLAST locally, I've downloaded the nr database via update update_blastdb, I've added .ncbirc to the home folder which has [BLAST] BLASTDB=/home/bioinformatics/Desktop/blastDBand yet when...
View ArticleComparing Bowtie H_Sapiens_Asm Blastn -Task Blastn-Short -Db Human_Genomic
I am thinking the current supplied (pre-formatted) blastn humangenomic database from NCBI contains many many duplications of the same sequences. Is this correct? I think I only need the current...
View ArticleBlast Result Matching Both Of Two Query Sequences?
If two short sequences (A and B) come from the same gene, but I don't know the name of the gene or the organism, can I perform a BLAST (or similar) search to find the gene which has best similarity...
View ArticleBlast Text-Output To Xml Converter
Hi, I'm looking for simple way of converting blast output in text (stardard output) into XML format (maybe some has got script?). I've looked elsewhere but couldn't find anything:/UPDATE I ended up...
View ArticleI am running blast over internet using biopython but its giving connection...
import Bio import csv from Bio.Blast import NCBIXML from Bio.Blast import NCBIWWW q_id = [] with open('C:\Users\Nadia\Desktop\imran-sequenceIDs.csv','rb') as f: reader=csv.reader(f) for row in...
View ArticleGenerating Protein Consensus Sequence For Blast Input
I have a set of 3 protein sequences for which I need to find the "consensus sequence" which can be used as an input to blast against a local database.how should I go about it?
View ArticleBlast2Go Statistics
HI When I run blast2go I want to receive statistics about how many sequences fit to each category. When I go to statistics in the blast2go I only manage to generate graphs. How can I receive the data...
View ArticleDefault Ncbi Blast+ V. 2.2.25 Parameters
Hi:I'd like to compare my own BLAST tool with NCBI blast+ tool but couldn't find the default parameter of this version. I'd like to know the scoring scheme for match, mismatch, opening gap and extended...
View ArticleHow to use whole computer cluster power for computation of a single job?
I know the computations by breaking the files and parallelize it in SGE or SLURM. I want to use whole computation power (20 node , 80 cores) for a single job without breaking it. If I just submit it (a...
View ArticleLooking For A Command Line Version Of Ncbi Taxonomy 'Stratification' Tool
Hi allI am building a pipeline for taxonomically identifying a blast result at each taxa level, with a bespoke reference dataset. I want it to be easily reproduceable, which it is, other than an ugly...
View ArticleExtract 100 Downstream Sequence Of The Aligned Sequence Of Blast.
Hi all,I need to get 100 downstream of the nucleotide sequence from aligned results of the web blast query.Is there any way to get the required sequence from NCBI?
View ArticleTools Parsing Ncbi Blast -M 7 Xml Output Format?
Hi all,Is there any script or tool which is able to parse NCBI blast xml output (produced with -m 7 option) ?I want a tab delimited file containing the following information: Name of the query sequence...
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