Changing evalue doesn't change the results of blast
Hi! First's run results occurred by this command : tblastn -query query.fasta -db plant_DB -out output-evalue -html and in some reads i got two targets. e.g : Score = 160 bits (404), Expect = 1e-44,...
View ArticleFinding Pdb Codes Of Sequences Homologous To An Input Sequences
I need to write a script that can do a blastp with an input xml file, then find and display the PDB codes of sequences that are homologous. The definition I'm using for homology is: 1. the HSP in the...
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 ArticleBlast Alignment Bug
I tried to find a short oligonucleotide sequence (probe) in a transcript and I knew for sure that the transcript contained the probe. But the latest version of the BLAST stand-alone algorithm (2.2.25+)...
View ArticlePrimer design using Bioinformatics tools.
Hi, I am currently working on a project designing a primer template for detecting any pathogenic species of leptospira in a serum sample, but I seem to have hit a roadblock. While the ncbi primer...
View ArticleComparing Blast M8 Outputs
Hi,I want to compare BLAST outputs in m8 format to find out if any queries in the separate output files have the same subject hits to NCBI nr database.For example, for the 2 BLAST outputs in m8 format...
View ArticleWebtool For Fetching Pmids From Blast?
Hi, I was wondering if there is a web service that extracts all of the PMIDs that are in the results for a BLAST search? Example: I input the sequence for enchanced FLP and get a list of all the PMIDs...
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 ArticleBlast: Influence Of Database Filesize On Performance, And Purpose Of...
Obviously BLAST is going to have better on-average performance on a smaller database than on a larger database. But for a particular (large) database (let's say 10s of GB), how does splitting up the...
View ArticleWhat Is The Lowest E-Value In Blast When Ncbi Rounds It Down To 0 (Zero)?
Hello, Just out of curiosity, an E-value of more significant hits in BLAST approach 0, but cannot equal 0. In some cases when the E-value of a HSP is very low NCBI BLAST rounds it down to 0. What is...
View ArticleExtract Specific Entries From Blastx Output File, Write To New File
Hello, I have created a script that successfully searches for keywords (specified by user) within a Blastx output file in XML format. Now, I need to write those records (query, hit, score, evalue, etc)...
View ArticleBlastp And Biopython
I have noticed that when I blast my own database in particular some of the sequences get truncated. This is using my local blast algorithm.For example I know that the sequence FYNTSTPQ and FYNTSTRR...
View Article. [Blastall] Warning: Unable To Open Bos.Db.Nin
I created the database of 1 chr using makeblastdb tool of localblast. It showing me output, But it also showing me warning while i am blasting from programming. that ..[blastall] WARNING: Unable to...
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 ArticleError While Running Standalone Blast Via Bioperl
Dear All,I am trying to run a stand alone blast in my system. I have created a database locally and I am tying to run the blast against them using STANDALONEBLAST module of bioperl. The code is as...
View ArticleBlast Display Non-Matching Ends Of Sequence
Is it possible for blastn to show the parts of the database which do not match? Eg if I ask blastn for matches to a 36 base pair sequence and it finds a human DNA sequence which matches 27 bases of 30,...
View ArticleIncomplete Blast Database In Ubuntu
hello all, i am trying to do local blast using this command blastall -p blastn -n T -i query.fasta -d nt.12 -o /blast.outi am doing a "blastn" , "-n T" shows i want to megablast. i have downloaded...
View ArticleAligned Ranges In Blast
I have several sequences which I'm blasting against the nt database, and I wanted to know how to retrieve for each hit the intervals matched. As far as I'm aware, the standard output only gives this...
View ArticleLocal Blast Returns No Result, While Using The Website There Are Some Matches
I want to blast some EST with local blast. However, for some sequences, there are no matches while with the website http://www.arabidopsis.org/Blast/index.jsp.(I download the database from the site,...
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...
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