Blast+ Stand Alone Version For Sequence Alignment
HiOn the on line version of Blastp (link text) there is a sequence alignment section (and it produces E-values for the alignment).and now I want to use the standalone version to perform alignment(My...
View ArticleProblems Using Formatdb And Fastacmd
Hello!!I am having an extremely difficult time with formatdb and fastcmd from NCBI blast.I am trying to make a db from single mouse chromosome from NCBI using formatdb. Afterwards I try to obtain...
View ArticleNcbi Blast Output Missing Subject Name
I'm wondering if anyone has stumbled upon this issue I'm having with blast. I have a set of contigs I'm blasting against NCBI's NR blast database, and the blast report I get back has a blank field for...
View ArticleBlastall gives several hits to the same subject sequence
Short query sequences will sometimes give several hits to the same (often large) subject sequence. This is problematic if you ask for the 20 best hits since blastall will actually give you the best...
View ArticleTaxonomy Of Blast Hits
Lets have 200k genomic contigs with some (unknown) bacterial contamination. I blasted (blastn vs nr) all of them, got tabulated output and passed the uniq acc nos ca 5k to Batch Entrez. Since neither...
View ArticleHelp! I Can Successfully Run A Blastp Search In Bioperl But I Want To Also...
I am new to Perl/Bioperl and have run into a problem. How can I perform a blastn search on a DNA sequence? I can successfully perform a BLASTP search, but I can't find any documentation in cpan or...
View ArticleIn biopython, how can i get the 100% identity aligment?
I find the way to get the identity of hsp ,but no alignment.One alignment can have multiple hsp, that means the score(identity) of hsp is no equal to alignment. when i do blast in webpage, i always get...
View ArticleNCBI GI to Gene Description
Hello all,I have a very large list of NCBI gene IDs (such as, gi:47221249, ect). I am hoping to use this list to get the descriptions for each of the gene IDs. Using the GI above it would be "unnamed...
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 ArticleDefault Frameshift Penalty For Blastx
I do not set the frameshift penalty costs and output everything in BLAST XML format. Then I go through this file and usually the beginning contains parameters of the scoring scheme etc. But it does not...
View ArticleMasking repetitive sequences ...can I then map using BWA?
Hi thereIn need of help please!I'm masking the repetitive regions in my wheat sequencing data using RepeatMasker. This generates a .masked file. Next I want to map or compare this masked file to other...
View ArticleTo Do Blast Alignment Of Two Proteins By Biopython
I am new to biopython and I am not sure if it is a stupid question.I would like to perform the same task as the one can be done on the web based blast. I am trying to align two protein by providing...
View ArticleHow To Prove An Ortholog Does Not Exist In A Given Genome?
I am wondering what is the best way to prove that an ortholog is absent (or at least un-identifiable) from a given sequenced genome.My initial thought goes to a tblastx search, where an absence of...
View ArticleGet Pairwise Sequence Identity
Hey,for some project I need to run pairwise sequence alignments (local ones, i.e. Smith-Waterman) on protein sequences in order to produce a similarity matrix based on the percentage of identical...
View ArticleHow To Remove All Sequences In My Custom Blast Database?
Is it possible to clear a blast database once you have made it? I mean I created my custom database with nucleotide sequences, but I think I messed up something so I need to empty/clear my database and...
View ArticlePython Program Accepting Fasta And Blast, Outputting In Xml Then Returning...
Ok. The assignment was to write a program which accepts an input argument of a FASTA file and prints the hit_id of all found sequences using three functions: run_blast (accepting the FASTA and optional...
View ArticleHow To Blast A Nucleotide Profile (Pssm) Against A Nucleotide Database?
I saw that tblastn is capable of doing that kind of search, but I want my position-specific scoring matrix (pssm) to be built from nucleotide, not protein, sequences.Has anyone done something similar...
View ArticleRecovering Positions Of Identical Matches From Multiple/ Pairwise Sequence...
I would like to do a pairwise/multiple sequence alignment for a gene from two/three species and then record in a separate file the exact positions of perfect identity between the sequences. Is there a...
View ArticleBioperl Has Different Behaviours In Parsing Blast And Blast+ Result
When I was using BioPerl to parse the blast results, I found that it can parse the blast(2.2.21) result but not the blast+(2.2.25+) result(all were in the default format). The parser.pl code:...
View ArticleThe Meaning Of The E In Blast Output
I have a question that's been floating around in my head for a while, and a colleague recently asked the same thing so I thought I should finally get to the bottom of it.What does the 'e' in the output...
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