Low Stringency Blast (To Find Outgroups)
Hi!I'm looking for a way to find appropriate outgroup sequences for my paralog phylogenetic tree. Is there a way, using blast, that I can find sequences that are only a little similar to my query...
View ArticleHow Set A Pssm (Position Specific Scoring Matrix) When Querying With Blast+?
help me out if anyone knows the answer for my question, How to search a nucleotide database using PSSM ( i developed the PSSM using set of protein sequences from query set) Do provide me the command in...
View ArticleHow Can I Determine Whether Two Proteins Have The Same Multi Domain...
How can I determine whether two proteins have the same multi domain architecture? For example, if I do a BLAST search for proteins with high alignment scores, what can I do with the resulting list of...
View ArticleNcbi Refseq Viral Genomes
I want to create custom blastdb with all viruses available in the refseq. But I don't know which source files to use. My first point is:ftp://ftp.ncbi.nih.gov/genomes/Viruses/From research I concluded...
View ArticleCorrect 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 Report: Expect(2) = number instead of Expect = number, what does it means?
Hi all, in the sample below is shown two alignments with Expect and Expect(2) report: Score = 248 bits (129), Expect = 1e-63 Identities = 213/263 (80%), Gaps = 34/263 (12%) Strand = Plus / Plus Query:...
View ArticleAlignments As Queries In Blast
Hi guys, i'm reading a paper and i'm not understanding the following note:Alignments were made using IGRs (intergenic regions) from S. meliloti as queries in BLAST comparisons against the...
View ArticleWhat Is A Good Web Front End For (Blast) Homology Search?
One fairly common task is to make some sequences available for BLAST search over the web. So far, this has meant installing the NCBI web front end to BLAST, but this is something like 15 years old, and...
View Articleblast FATAL ERROR: BlastFormattingInfoNew returned non-z
Hi,I'm running blast commands from a cluster of nodes and sometimes if succeeding and sometimes it fails.the command i run is:blastall -p blastn -g F -q -9999 -i...
View ArticleHow To Get Fasta Source File From Blast Csv Format?
I am currently writing a library that uses the -outfmt 10 option of Blast, which give you a CSV instead of the pretty human readable format.Liketblastn -db dmel_a -query somequery.faa -outfmt 10The...
View ArticleHow To Use Biopython To Parse Blast Output And Get Gene Symbol From Ncbi?
Hello all. I am very, very new to Python/Biopython and am currently stuck.I am using standalone BLAST via Bash. I have about 40k non-human sequences which I am blasting against the human genome,...
View ArticleOrf Finder Vs Blastx
This is kind of a stupid question. Suppose I have a contig sequence and I want to know what kind of protein it might encode (if it does). I run it against NCBI ORF Finder and then choose to do a blast...
View ArticleBlast - Formatting Output
Hi,I've been using the blastn (version 2.2.28+) standalone tool against a custom formatted genome via:blastn -db BLASTDB -word_size 7 -query input.fa -out filename -perc_identity 100 -outfmt 6...
View ArticleParse Blastdb Format From Java
Does anyone know a java library to parse blastDB files? I've found the specification at http://selab.janelia.org/people/farrarm/blastdbfmtv4/blastdbfmt.html for the file format, and the code for a C...
View ArticleHow To Blast A Sequence Against Multiple Databases
Hello,I have downloaded all the chromosome of Bos taurus and I have changed them in blast format using makeblastdb..and now I want to locally blast my sequence against these all chromosomes. now I have...
View ArticleError Running Blast2Sam.Pl
I am trting to convert blastn (from blast-2.2.25+) output to sam format using samtools "blast2sam.pl" script.Any suggestions to rectify the error?Error message:Use of uninitialized value in subtraction...
View ArticleSequence Blast Against Rfam Database
Hi All,I am using blastn to blast my data against tRNAs which is extracted from RFam database. Then I picked one match from the blast result to confirm it by directly searching my read in RFam online...
View ArticleIs It Possible To Get Near Global Alignment From Blast?
Hi to all When a query sequence identical to a database sequence is done BLAST, the alignment is shown for 100% of the sequence ie.complete coverage. Cannot this situation may be said global alignment?...
View ArticleCan Ncbi Blast Only Search A Special Region In Database For Hits?
I want to blast my 36SE reads to a special region of HG19, does NCBI BLAST can do this special region search? If so, how can I do this?for example, I only want my reads to be blasted to chr1:5000-10000...
View ArticleParse Blast Output ..
i want to parse this blast output but compilers giving NULLPOINTEREXCEPTION .. input file and source code of java program is given below ... plz help me out..Exception in thread "main"...
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