Correct Method To Blast All-Vs-All With Ncbiblast & How To Speed It Up?
Hi all,I'm using ncbi-blast-2.2.24+ (on Ubuntu linux) for a sizable all-vs-all blast of protein sequences (530.000 lines of fasta). This is taking quite a while (over an hour) already, so I'm looking...
View ArticleBlast A Specific Contig Against Multiple Contigs From Another Organism
I have a contig from one organism that is of interest. I have been searching this contig against another organisms complete collection of contigs found on NCBI by using an online DNA translator and...
View ArticleAre old versions of NCBI's nr stored somewhere?
Hello,I'd like to study how NCBI's non-redundant protein database (nr) has developed over the years. However, I'm yet to find a way to download anything but the latest release from the NCBI ftp. Are...
View ArticleBlast+ Error: Sequence Not Returned
I'm getting an error when running blastn against the nt database:Error: (117.2) CThread::Wrapper: CThread::Main() failed NCBI C++ Exception: Error: (CSeqDBException::eArgErr) Sequence not returned.The...
View ArticleHow Can I Download The Results From An Ncbi Blast Search?
I'm BLASTing a sequence on NCBI (http://blast.ncbi.nlm.nih.gov/Blast.cgi#), I see a page of results showing the portions of the sequences that aligned to my search sequence. I now want to download...
View ArticleHow To Make Pssm With Makeblastdb
i want to make a pssm from a fasta file for searching with rpsblast, i have the 2.2.23+ version of blast, so formatdb is replaced with makeblastdb. I have used it to make a database from the genome im...
View ArticleNcbi Standalone Blast -Outfmt
Hi,I want to include the % of query coverage in my standalone blast result. Can anyone help me with this ??RegardsBHARAT
View ArticleExpanding Multiple Sequences In Fasta File
I have a fasta file with sequences of about 100 amino acids and i need to expand them on both sides with the corresponding amino acids to get a fasta file that contains the entire domain sequences...
View ArticleBlast 2.2.24+ Database Error
When running local BLAST on a big database (all human proteins) I get the following error:proteinsApplicationError: Command 'blast-2.2.24+/bin/blastp.exe -query "query.fasta" - db...
View ArticleExtract only viridiplantae genes form swissprot
I want to use only viridiplantae genes in the SwissProt database. Using TagIdent I was able to sort of filter, but now I don't know how the either download these genes, or take the IDs and filter...
View ArticleDistribution of e-values in Best Reciprocal Blast Hits for Ortholog Mining
Does anyone have an idea of how the distribution of expect values will look when using reciprocal blast to detect orthologs?
View ArticleBLAST definition and difference between 'qcovs' and 'qcovhsp'
Hello,Can anyone provide a clear definition of what exactly the BLAST+ output parameters 'qcovs' and 'qcovhsp' are? From the help pages:"qcovs means Query Coverage Per Subject""qcovhsp means Query...
View ArticleMakeblastdb Help
Hi,I feel I'm being really dumb here, so please excuse me! I have a file of fasta sequences which I want to make into a blast databse for standalone blast.I haev the fasta file saved in the bin folder...
View ArticleBLAST: How much of the query is aligned?
At first, I thought this question would answered by the "qcovs" field, but a glance at the results proved that that isn't the case. To begin with, each qcovs value relates not to the original query,...
View Articleblast output using -6 format option
Hi,I am running a local blast and save my output using -6 format (tabular). For one hit the result is displayed fine, however for more than one hit, for example when I have two hits, the second result...
View ArticleIs There Such A Way/ Program To Do This...
Hi guys,I followed the Trinity/ RSEM/ EdgeR pipeline and have produced some FPKM spreadsheets for genes and isoforms.I am currently analysing the isoforms:I have 3 sample conditions and I am comparing...
View ArticlePros and Cons of HMMER versus BLAST
Hello everyone,I'm searching a set of bacterial proteomes for a family of genes that undergo frequent HGT and domain restructuring, such that homologs in closely related species may appear quite...
View Articlede novo RNA-seq and different assembly options
Hi all -- I'm new to RNA-seq and have had some issues assembling the reads. I'm looking for any advice or input on what might be the best way to handle my data. My work is done in oocytes of a...
View ArticleTO BLAST LARGE QUERY SEQUENCE AT ONE TIME
hi community, i have near 4000 query sequences that i need to BLAST inorder to find homology. to do this should i need to blast my query sequence 4000 times individually one by one or we have any...
View ArticleHow To Convert Blast Results To Gff
I'd like to visualise the results of a BLAST search in a genome browser. Is there a simple way to get the results in GFF format without having to write a parser myself?
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