How to analyze the ProDom output? I have some results to support the...
Hi all, I have some results retrieved from ProDom database and I need to analyze the output from 3 inputs to check if they share the same conserved domains, the results points to same description of...
View ArticlePipeline Or Tool For Going From Assembled Genome Fasta & Gff Files Directly...
I'm hoping this doesn't come off as a lazy question, but I am wondering if anyone is aware of a tool or pipeline out there that directly takes reference genome (supercontigs, contigs, scaffold, what...
View ArticleHow to add additional common names to a blast database
blastn with nt as a database can also return scientific name and common name of the blast hit viasscinames and scomnames in outfmt.I can get that also if I make my own blast database if I add-taxid_map...
View ArticleMultiple Blast Output Formats From 1 Blast Run
Is it possible to generate 2 different output formats (tabular and the default one) by running blastn just once or I have to either1) Run it 2 times - one for each desired output2) Generate the tabular...
View ArticleFilter command-line BLAST results by organism
In legacy blast (blastall) it was easy to do a remote BLAST query from the command line that only returned hits for a single organism: blastall -u "[Arabidopsis thaliana[organism]" -p blastp -d nr -i...
View ArticleDetermining Orthologs With Best Reciprocal Blast Hits For Mrna
I have typically been using tblastx when using mRNA, is this correct?
View Articlesequence BLASTed against itself.... why?
I am reading a paper that describes the identification of "single copy genes" in plant species.I'm trying to understand why the below described process is useful:"To establish a useful criterion for...
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 ArticleNcbi Web-Blast With Huge Subject Sequence Provided By The User In Fasta File
hello everyone,I tried to blast my query sequences with my subject sequences in fasta file...i uploaded both my query and subject sequences in fasta file to the ncbi blast page, but it didnot...
View ArticleTutorial: Installing And Running Ncbi Blast
##rest "Installing and Running NCBI BLAST" tutorial imported from the MSU course Analyzing Next Generation Sequencing Data (http://bioinformatics.msu.edu/ngs-summer-course-2011) You should start this...
View ArticleStandalone blast results wrong
Hi,I downloaded the NR database from NCBI about 2 months ago. The past few times I have run a blast search on some contigs, the results have been wrong on many of the query sequences. I checked this by...
View ArticleOrthomcl Blast Error: No Hits Are Being Saved
when i try to run blast in orthomcl using the command below:blastp -query goodProteins.fasta -db goodProteins.fasta -evalue 1e-5 -out goodProteins.blast -outfmt 6 -seg yes -soft_masking true...
View Articleconvert legacy blast parameters to blastn
Hi all,I am following the parameters given in a paper for performing blast.The parameters given are in the old format; -X 150 -q -1 -F FCould anyone convert them to the current blastn format?eg...
View ArticleLimit 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 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 ArticleHow Can I Automate Blast Of >1 Sequence And Output The Top Hits For Each Input?
I'm looking for a way to do BLAST simultaneously with >1 sequence. The input is several fasta files or one file containing several sequence formatted in fasta. For an initial testing, I want to try...
View ArticleFind Mismatch And Gap Positions
Hi everyone,I want to find the homologs of many short sequences, and then identify the mismatch and gap positions for each pair. The first step can be easily done by BLAST, FASTA or patscan, but the...
View ArticleQuick Command To Split Large Blastx Files?
Any thoughts? I have large 7 gb files as resulted from Blastx any clue how to split them?Edit:These are standard blastX files (fasta). I need to split them for a program (binning) call SOrt-ITEMS/MEGAN
View ArticleHow To Force Blastp To Display All The Possible Combination Of Alignments?
I want to use blastp to find out all the alignment among two fasta file.Here is my command:blastp -query "A.fasta" -subject "B.fasta" -evalue 1 -outfmt 6 > output.txtI have already set the e-value...
View ArticleUsing Blast2Go From The Command Line
Hi,I am looking for a way of using Blast2Go on a remote server in a more or less FIRE AND FORGET manner. My idea is to use either a command line version of Blast2Go or an API that would permit me to...
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