Blastp With Just Top Result From Each Organism
(My first Q on biostar, forgive any transgressions please!)I would like to blast a protein/aa sequence and filter(?) my results to include only the top result from each organism. I'm keen to use R or...
View ArticleA query on pre-miRNAs
I copied this line out of a paper. Firstly, all the known pre-miRNAs in the training set are used as queries to BLAST search against the genome with a sensitive BLAST parameter setting (word-length 7...
View ArticleStandalone BLAST with kingdom classification
Hi all,I have an assembled transcriptome from an organism hosting various symbionts and I'm now interested in how many of my contigs hitting to the different kingdoms. What I've found so far is 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 Generate A Species Distribution From Blast Xml Output
Hi,I am very new in bioinformatics field. I have a BLAST XML output file and I need to parse it to generate a species distribution. I was hoping someone could show me how it can be done by Biopython...
View ArticleBlastn / Tblastn : Mapping The Features Of The Query To The Hit.
I'm blasting+ (blastn+ or tblastn) an annotated sequence (a Genbank.xml sequence (nucleotide or protein) or an Uniprot.xml entry) against a DNA database.Is there a standard tool to map the features of...
View ArticleDownloading And Maintaining A Local, Blast-Able Nr Database
I am planning to set up and maintain a local version of the NR and other NCBI databases, for running in-house BLAST searches. I would also like to my local version of the databases be in synch with...
View ArticleQuery Vs. Target Using Blast2
I'm running blast2 locally using DNA sequences in fasta files. I have one large target and a load of smaller query sequences.Version: 1.2.2.21.20090809-1 (blast2)blast2 -p blastn -r 0 -q -2 -G 2 -E 2...
View ArticleHow Can I Determine Whether Two Proteins Have The Same Multi Domain...
How can I determine whether two proteins have the same multi domain architecture? For example, if I do a BLAST search for proteins with high alignment scores, what can I do with the resulting list of...
View ArticleAnnotating Sequences For Gbrowse - Which Is The Database And Which Is The Query?
Let's say I have some small sequences that I wish to display in Gbrowse. I want to create tracks from Blast results to show where genic regions might be.Do I create a Blast index of the small sequences...
View ArticleBlast E-Value To Database Size
Hi,I'm thinking of splitting the database to smaller chunks. And, blast my sequences against them each on a separate process. My only concern is the results (which I will merge later).Would the...
View ArticleError in run blastpgp
Hi, I am trying to have the command line blast work, however, I did not manage to execute it properly. I would appreciate if you can tell me what I am doing wrong. So here are the things I did so far:...
View ArticleBlast E Value Calculation
I'm trying to work out the formula for BLAST e value calculation. I have surfed all across the internet looking for it, but the only thing I'm able to find is the formula provided here:...
View ArticleError Using Makeblastdb
Hi there,I am trying to run makebastdb to create a new BLAST database. The program starts but cuts out abruptly with an Error:Error: ncbi::s_FixBioseqDeltas() - Bioseq must have Seq-data or Delta...
View Articlelocal or remote blast BLASTp against pdb database (formatdb)
I want to blastp protein sequence file (>3000 sequences) against PDB database for generating templates for Homology modeling. Please help!!I tried remote blast and local blast using formatdb but...
View ArticleOnline Blast Perl/Python Script
Hi AllI have a 10000 sequences in fasta file which I want to do online blast with nr data base . Do any one of you has any perl or python script to do that?Thanks in advanceRegards
View Articledata from SRA against blast databases method.
Hello.I want to find a specific gene inside SRA files and I am wondering if i am using a correct way to align those sequences because its the first time that i am "playing" with something like that.So,...
View ArticleAny tool to generate protein similarity matrix
Hi, I want to calculate the similarities between each protein pariwise and then implement random walk to predict interactions. A paper mentions "J. Mol. Biol. (1981) 147, 195-197" to compare two...
View ArticleBlast Illumina Probe Sequence To Get Their Genomic Coordination
Hi all, The annotation file provided by Illumina for RatRef Expression chip is poorly annotated. Since illumina stopped selling these chips they stopped updating their annotation as well. So I am...
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...
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