Running Blast For A List Of Pairs
Hi,I would like to ask if it is possible that I run BLAST with a list of pairs of query and reference sequence IDs?I tried bl2seq but unfortunately it does not produce the alignment of the whole...
View ArticleComparable E-Value Among Blast Programs
If I specify the search space via -dbsize flag among blasts of the same query to multiple databases, the e-values will be comparable among all the results because the search space will be...
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 ArticleMakeblastdb Error
I get this error when trying to make a database from fasta file:BLAST options error: blastdb.FASTA does not match input format type, default input type is FASTAhere is sample of my...
View Articlelocal tblastx error
Hi, I am getting following error while running tblastx against NR database “BLAST Database error: No alias or index file found for nucleotide database [/data/ncbi/blastdb/nr]My seq is nucleotide, Blast...
View ArticleFASTA-Reader: First data line in seq is about 100% ambiguous nucleotides...
I am not sure if this is a problem or if in fact the process is correct. Any help is much appreciated. I am trying to make blast databases from assembly fasta files, and have seeing the above error. It...
View ArticleShowing Queries With No Hit In Tabbed Blast Output?
Hi, I was wondering if anyone could tell me if there's a way to get the tabbed BLAST output to show if there's not hit. I don't mind using either blastall or blast+.The reason I ask is that I'm trying...
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 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 ArticleComparing Assemblies
I'm working with two transcriptome assemblies. They're essentially different versions of the same transcriptome, one of them just includes more data and is therefore (presumably) better quality. A...
View ArticleIs there a good service for annotating transcripts?
After getting say 100k transcripts from an rna-seq project, generally one wants to annotate them against a database like nr, using say blastx. Problem is, this is very slow, taking e.g. a week with 24...
View ArticleDetermining Orthologs With Best Reciprocal Blast Hits For Mrna
I have typically been using tblastx when using mRNA, is this correct?
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 ArticleMethod Of Getting Progress Of A Blast Run
Are there any parameters in blastall that'll make the program inform the user of the current progress of the blast run?
View ArticleStrategizing Blast Result Parsing
I have a set of ~200 known sequences of a particular domain that I want to use to fish out similar sequences from NCBI-NT.As you can imagine, my blast results for this dataset are redundant in the...
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 ArticleAny Way To Ncbi Blast Multiple Protein Sequences?
Is there any tools or any direction anyone can point me in towards Blasting multiple amino acid sequences on http://blast.ncbi.nlm.nih.gov/Blast.cgi ?I could potentially write a script to do this and...
View ArticleRepeatmasker Crashes Before End Of Run With "Can'T Fork..."
I've been trying to run RepeatMasker but it keeps crashing with the error "Can't fork...". In the RepeatMasker script source code, this is here:FORK: { if ( $pid = fork ) { $flag = 1; waitpid( $pid, 0...
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 ArticleSpecies-Specific Output From Blast -Db Nt -Remote ...
I'm using the C++ version of blastn, with -db nt and -remote. I need to limit my search to a specific organism. I've had success using -gilist <file> to do this on searches with a local database,...
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