Taxonomy Of Blast Hits
Lets have 200k genomic contigs with some (unknown) bacterial contamination. I blasted (blastn vs nr) all of them, got tabulated output and passed the uniq acc nos ca 5k to Batch Entrez. Since neither...
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 ArticleWhat Is A More Meaningful E-Value For 90Bp Pair-End Illumina Data?
Hi all, I used to use e-value <= 1e-5 for getting any meaningful blast alignment results. Just saw this statement in BLAST FAQ"The lower the E-value, or the closer it is to zero, the more...
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 ArticleConcatenating fasta files for BLAST
I have two fasta files from WormBase. One is the coding transcripts, the other is ncRNA. When I BLAST (using NCBI Blast+) 44k 60-mers against just the transcripts, I get 37,216 hits. When I...
View Articleblastn cannot find the database
I'm new to BLAST and am trying to run a legacy blast command using blast+. I have downloaded the human_genome databases and unzipped and untarred them.The databases are in:...
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 ArticleProblems Using Formatdb And Fastacmd
Hello!!I am having an extremely difficult time with formatdb and fastcmd from NCBI blast.I am trying to make a db from single mouse chromosome from NCBI using formatdb. Afterwards I try to obtain...
View ArticleAligned Ranges In Blast
I have several sequences which I'm blasting against the nt database, and I wanted to know how to retrieve for each hit the intervals matched. As far as I'm aware, the standard output only gives this...
View ArticleBlast Output Into Jsp/Html
I would like to display a blast result in a jsp or html by parsing the xml result of blast without using BioJava? how can I do that?
View ArticleApplying A Pssm To Psi-Blast
I'm able to generate a PSSM and a sequence from combinatorial experimental data. I want to BLAST the results to find proteins displaying these motifs. However, I have information about each position's...
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 ArticleBlast a gene against one genome
Hello,I want to run a blast of one gene against one genome. I have a fasta file of them both. Is there any way to run it other than converting the genome to a DB file?Thank you in advance
View ArticleBlastdbcheck Error
I keep getting errors on the following command:blastdbcheck -db nt.00Writing messages to <stdout> at verbosity (Summary) ISAM testing is ENABLED. Legacy testing is DISABLED. By default, testing...
View ArticleI am running blast over internet using biopython but its giving connection...
import Bio import csv from Bio.Blast import NCBIXML from Bio.Blast import NCBIWWW q_id = [] with open('C:\Users\Nadia\Desktop\imran-sequenceIDs.csv','rb') as f: reader=csv.reader(f) for row in...
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 Article" ERROR: ObjMgrNextAvailEntityID failed with idx 2048" when using blastpgp
I am running blastpgp using as query a .faa file containing around 31.000 seq. My db contains also more than 50000 seq, and I select -m 9 to have a tab del output. During the run I get the following...
View ArticleHelp With Bioperl Remote Blast Script (Bio::Tools::Run::Remoteblast)
Hi, I would like to run a blast search for a fasta file containing many (100+) seqences. I wrote a test script and ran it using a test query file (contains only one sequence; fh= diffexp1). If my code...
View ArticleMachine Spec For Running A Blast Service For ~50 Users
I have been asked this question by a friend, but I didn't feel I could give a satisfactory answer. Maybe somene here at BioStar can share some experience.The question is: what kind of hardware would...
View ArticleHow To Parse Psiblast Results Using Biopython And Blast-2.2.24+?
I'm trying to run a PSIBlast program which selects certain sequences out at every round before it does the next iteration. For this I need the Round attribute shown in...
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