Why does Blast report a different alignment when using the -m8 option
i really need to know why when i do a blast with the option -m8, i have different results (different % identities, and gaps). example..normal >tr|Q3T560|Q3T560_9GAMM Arsenite transporter ATPase-like...
View ArticleGet Blast Database Size
I have piped unknown length sequences into makeblastdb. Now I want to know total length of those sequences (BLAST database size).Example: # "cat" is used as an example # My "real" sequences are piped...
View ArticleBest Blast Hit Without Pain
Hi,This might be naive but here I go. I have a set of target sequences and a query sequence. I want to find the best BLAST hit (lets say using the bit score). The straightforward way to do this is to...
View ArticleBlast Contigs To A Reference Sequence And Obtain An E-Value
Well, I'm a newbie of blast, so...hope I'm not asking a stupid question....I've already have a set of contigs which is done by de novo assembler. Format of these contigs is fasta. Now I want to align...
View ArticleE-Value In Blast
Hi all:I am calculating my e-Value for my own BLAST alignment. I used the formulae: e= mn2^-S'where: m = length of the query sequence n = total number of lengths of all template sequences in the...
View ArticleNcbi Blast+ Taxid And Taxid_Map
2 related questions. How does the -taxid argument for the NCBI's blast-2.2.24+ makeblastdb command work? When I execute:makeblastdb -title "BO" -dbtype nucl -out BO -in BO.fna -parse_seqids -taxid 3712...
View ArticleBlastdbcheck Error
I keep getting errors on the following command:blastdbcheck -db nt.00Writing messages to <stdout> at verbosity (Summary) ISAM testing is ENABLED. Legacy testing is DISABLED. By default, testing...
View ArticleDetermining Orthologs With Best Reciprocal Blast Hits For Mrna
I have typically been using tblastx when using mRNA, is this correct?
View ArticleWindows Cmd Not Responding With Python Blastall 2.2.17
I'm using the standalone BLAST 2.2.17 with python. However, I'm having a problem with the cmd. When running the script the cmd stops responding at the 15th blast record. It doesn't matter if I change...
View ArticleCombining stats of multiple BLAST queries
Hi all,I have a FASTA file with let's say following structure:>Query_1 actgacgac....>Query_2 gtacgatcagct...I want to BLAST this FASTA file against a set of databases one by one and combine the...
View ArticleVertebrate Subset Nr Database? Build My Own?
I think I have the answer to my own question, but I'm somewhat new to bioinformatics, and I want to make sure my strategy is sound (and that there are no easier solutions to my problem). We need to...
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 ArticleBlast Runs In Unix Shell But Not Perl
I'm trying to run BLAST in Ubuntu 12.04, using a virtual box. It works fine in the command line, and produces the appropriate results using this blastn -query myfasta.fna -db nt -out output.outWhen I...
View ArticleNcbi C++ Exception: Ncbi::Cmemoryfilesegment::Cmemoryfilesegment() - File...
I have tried running a command line blast. The query file is a multi fasta file containing 2600 sequences. It was made a BLASTX against a proteins sequences (ProDom) of size 2 GB (prodom.phr : 1:00 GB,...
View ArticleMake A Custom Blast Library Using The Output Of Another Blast Result
Hi Biostar,I am working on a microbial gene annotation project and I am interested in taking a large number of sequences (say 20,000) and blasting them against the NR database. However, even with a...
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 ArticleDoes Ncbitblastncommandline Reads The Outfmt (Options 6, 7, And 10 ) Correctly?
I am trying to call tblastn_hits = NcbitblastnCommandline(cmd='tblastn', query=query_handle, db=db_handle, num_threads=6, evalue=0.001, outfmt="6 qstart qend evalue bitscore", dbsize=10000000,...
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 ArticleAlignment Matrix
Dear all,I have a problem with the following website:http://www.nature.com/scitable/topicpage/basic-local-alignment-search-tool-blast-29096More specific, I have a problem with the matrix (completely...
View ArticleGetting Exact Number Of Genomic Copies For A Specific Sequence
Hi all,I'm trying to retrieve a set of sequences that can be used for primer design. These sequences have some requirements, e.g. present in 4 different species, not present in a number of species on a...
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