Is there a way to run ncbi blastx so that its result will contain GO (gene...
I've already tried BLAST2GO and it is either running too slow or unable to connect to its database.So, I was just wondering if there is a way to run blastx in a particular way with some parameter so to...
View ArticleHow To Cluster Sequences Based On Blast Results?
I want to cluster a set of DNA sequences into families based on BLAST results. Is there any idea what software I can use to do it? Thanks!
View ArticleProblem Running Blast Jobs.
I started to run blast, locally on my machine, on 4 files with 1323, 210, 501, 166 fasta sequences each.For all jobs except the first one blast returned an error:blastall(7004) malloc: ***...
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 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 ArticleHow Can I Get Older Versions Of Psi-Blast Program?
Hi,Do you know how I can get older versions of PSI-BLAST.Right now, I've downloaded 2.2.26, but I need to use these parameters. (Pardon me for the irrelevants). blastpgp -i seq-file -Q...
View ArticleAny Local Gui-Guided Blast Tools?
Hi All,I am currently looking into local, GUI-guided BLAST tools. I stumbled upon BlastStation2 and was wondering if anyone has experience with it ? Are there any similar tools such as BlastStation2...
View ArticlePros and Cons of HMMER versus BLAST
Hello everyone,I'm searching a set of bacterial proteomes for a family of genes that undergo frequent HGT and domain restructuring, such that homologs in closely related species may appear quite...
View ArticleHelp To Blast Sequences Against Drosophila Genome In Biopython
Hi,I am trying to blast certain sequences (in fasta files) against the drosophila genome using the qblast operation provided in BioPython. From the documentations, I have figured out that the second...
View ArticleHow Is The Word Score For The Look-Up Table Determined For Blast?
I'm going over some slides about BLAST from an introductory course of bioinformatics. I don't understand how the words for the look-up table are scored. The query sequence is split up in words of 3...
View ArticleWhich Bioperl Module Can I Use For Parsing/Mining Blast Output?
Hi to all, I have blastx results (default output). There are some blast hits starting at frame 1, others starting from frame2,frame3, frame -1 etc. I want to collect all query IDs that blast in...
View ArticleHow To Generate Blast Database
Hello I downloaded some database in gemnomes/Bacteria ( ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Acetobacterium_woodii_DSM_1030_uid88073/ ) I want to use blast program. I have some problem. How can...
View ArticleHow To Blast Multiple Contigs To The Reference Database?
i have multiple contigs in fasta format after assembling the reads. i also have 33 reference genome sequences. i want to blast the query sample sequence to my reference sequences as well as the plasmID...
View ArticleWebtool For Fetching Pmids From Blast?
Hi, I was wondering if there is a web service that extracts all of the PMIDs that are in the results for a BLAST search? Example: I input the sequence for enchanced FLP and get a list of all the PMIDs...
View ArticleHow To Define And Calculate Cip ( A New Parameters For Blast Analysis Of Cip...
IN the paper “Improved criteria and comparative genomics tool provide new insights into grass paleogenomics " they said:To increase the significance of inter-specific sequence alignments for inferring...
View ArticleHow To Merge Contiguous Blast Hsps! (-M 8 Tab)
Hi, guys! I performed blastx (-m 8) using a query file of many sequences, and for each target sequence, the output contains many fragmental hsps of significance, and these hsps have overlap positions...
View ArticleHow To Blast Kegg-Only Data In The 'Nr' Database
Hi there,I dont have a locally KEGG database bought,but I want to Blast my sequences against only the KEGG part of nr db cause you know blast whole nr is really time consuming.Here is my...
View ArticleRemote blast+ skipping query sequences
Hi, I'm running a remote blast on the nr database using some contigs I've assembled and I've noticed that it is skipping many contigs. Here's the command I'm using to search:time blastx -db nr -query...
View ArticleObtaining A Maximum Number Of Blast Hits: Problem...
I am having trouble getting blast to give me "correct" results. I am trying to retrieve as many hits with e-value better than 1. I query the database with a sequence that should have several thousand...
View ArticleOrf Finder Vs Blastx
This is kind of a stupid question. Suppose I have a contig sequence and I want to know what kind of protein it might encode (if it does). I run it against NCBI ORF Finder and then choose to do a blast...
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