Limit the memory size of blast?
Would anyone tell me whether it is possible to limit the memory size in blast+/blastall search? If possible, how should we do it? Thanks!
View ArticlePython/Perl script for defining minimum coverage of blast match
Hi - does anyone know of a script that allows for a blast result to be filtered by the minimum total coverage of the query/subject that the alignment/s represent?I'm imagining a script that calculates...
View ArticleDefine BLAST XML Parser by DTD
I have seen many examples of using a DTD to validate XML documents, but I was wondering if they could be used to dynamically define a document at runtime. Specifically, I was wondering if a DTD and a...
View ArticleDetermining Orthologs with Best Reciprocal BLAST hits for mRNA
I have typically been using tblastx when using mRNA, is this correct?
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 ArticleBLAST XML Document Iterations
When running BLAST with one sequence against a sequence database there is only one iteration in the <Iteration> element, as in the value of Iteration_iter-num is one. For example:<?xml...
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 ArticleAssessing quality and accuracy of de novo genome assembly
All, I am curious whether anyone out there has a method for assessing the quality and accuracy of de novo genome assemblies? I am currently doing in silico simulations of de novo genome assembly from a...
View ArticleNumber of gene cluster from blast output
After parsing genbank file and blast output(xml file) using biopython library, how can I calculate the number of linked gene cluster at different stringent level (0 to 100) increment of 10. Example0...
View ArticleMake a dotplot from blast alignment
Hi all,I am a complete beginner with blast. I used the NCBI online service for aligning two sequences, and got a nice dotplot representation. Now I am running blast on my pc, and I would like to obtain...
View ArticleParsing BLAST results in Java
Hey guys, so I am in the process of creating a Java app with a GUI and all based on metagenomic analysis. So my question revolves around running BLAST searches and returning the results in the most...
View ArticleBLAST database size influence on number of significant hits
I have a set of gene sequences and specific sequence. cat genes.fa >Gene_1_chr1_1000_1200 ACGT... >Gene_2_chr2_3000_3400 TTAT... cat sequence.fa >Searchable_sequence ACGG... I want to search...
View Articlewhich vertebrate genomes available for BLAST?
Which vertebrate genomes are available for online BLAST, without the need to download them? There are only a few available through GenBank, more in Ensembl. However, many more vertebrate genomes are...
View ArticleBLAST against SRA dataset
Dear all, I have downloaded a number of SRA genomic seqeunce datasets. I am wondering if it's feasible to perform BLAST againt these datasets using a number of gene seqeunce. This analysis will...
View ArticleAssemble reads according to BLAST result
Dear all, I performed blast using ~200 gene sequences from reference organism against a draft genome dataset from related species ( containing 12million short reads(sr), each of which is 88bp). The...
View ArticleAssemble before BLAST or BLAST before assemble?
Dear all, I posted a similar topic recently. I have a few draft genome data, all of which contain roughly 12 million 88 bp reads. I also have ~200 genes from reference organism, and need to find...
View ArticleLow 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 ArticleGPU-blast vs Smalt
Hi, I am wondering if anyone has compared Smalt vs Blast. Two ways to use Smith-Waterman to map reads to a reference genome. I recently got a hold of GPU-Blast and was wondering if it might go the same...
View Articleblastdbcmd - Too many positional arguments , the offending value: %f - WINDOWS
Hey guys, I'm trying to use blastdbcmd - when I type the following on cmdblastdbcmd -db databaseBLAST -entry_batch -outfmt "%f" -out test_query.txtthe following error pops up:Error: Too many positional...
View ArticleBLAST output with Species name
Dear all,my question is very simple. I have reads from a human RNASeq and I would like to check for contamination on a specific virus family. So my pipeline looks like1) Align on the human genome...
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