Problems In Creating Pssm Using Psiblast
Hi, Everyone.Recently I am using PSIBlast to create PSSM.Command seems like this: psiblast -subject oneseq.fasta -inmsa alignment.fasta -outascii_pssm pssm.txtThe problems is Error: NCBI C++ Exception:...
View ArticleBy What Criterion Can We Screen The Blast Results?
I used to select the first several sequences as the ideal sequences I want to get. But there are cases that a lot of sequences with high scores and low evalues will retrieve after blasting. When it...
View ArticleSEED assignment (MEGAN5)
For me it is not clear how MEGAN assign the SEED classes to the sequences. In the manual, it says that it is made throughtout the identification of RefSeq id (accession number?). When I load my blast...
View ArticleScript Or Tools To Blast Primer Sequences Against Fasta File
Hi, I am looking for a script or tool to blasta all of my primer sequences against the reference fasta sequence. When i tried to use megablast i did not get any output eventhough those primers are...
View ArticleErrors In A Bioperl Script, Please Help Me To Have A Check, Thanks In Advance!
Dear friends: I have a blast report, and want to extract following information for each result(query): the Query_name, hit_number, name and description of the hit(HSP) with the highest identity. my...
View ArticleTool to map sequences and get genomic coordenates
Hello, Is there any software to map sequences against a genome and get genomic coordates/genomic ranges? I used several tools to get short sequences of ncRNA, but in the process i lost track of the...
View ArticleCan I Have Blast Return One Hit Per Species
Hello all, I've been long troubled with redundant blast hits from different strains of the same species, for example, E. coli. These hits (can be dozens to hundreds) mask hits from other species which...
View ArticleForum: Sequenceserver: Easily Deploy A Custom, User-Friendly Blast Webserver
Executive Summary: SequenceServer lets you rapidly set up a custom BLAST+ server with an intuitive user interface for use locally or over the web.Why we created it: We were frustrated with:too many...
View ArticleHow to understand which DNA strand is (5' to 3' ot 3' to 5') in the result of...
Hi!if a have such a result from a blast run, how can i understand if its in the 5' or 3' side of the DNA or protein strand ?> gnl|SRA|SRR456295.4505.2 FIHSSUW02H237H.2 length=250 Length=250 Score =...
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 ArticleBlast+ On Windows
I need to compile blast+ on windows.Can someone tell me how do i do this.I tried Visual studio 2010,but i get an error saying that some project tree builder is not found.I am a beginner so please be a...
View ArticleError Running Blast2Sam.Pl
I am trting to convert blastn (from blast-2.2.25+) output to sam format using samtools "blast2sam.pl" script.Any suggestions to rectify the error?Error message:Use of uninitialized value in subtraction...
View ArticleFinding Coordinates Of Genes In Genome
Hi GuysI think I have a very trivial question. I have a multi-fasta file of rRNA genes. I need to find their location in the genome. It will be easy to blast them but not sure how can I extract the...
View ArticleAn Error By Using Ncbi-Blast-2.2.25+ (On Windows)
Hi all I downloaded blast+ software package (for windows), and installed like theBookshelf; to run it i used this "ncbi-blast-2.2.25+/bin/blastn –query text_query.txt –db refseq_genomic –out...
View ArticleIs There A Query Parameter For The Online Blast That Would Filter For Hits...
Hello,I am running blastn, blastx and tblastx searches on NCBI's nt, est, nr and HTGS databases using transcriptome data containing ~56,000 contigs. I have been able to produce biopython scripts to run...
View Article/Home/Abc/Ncbi-Blast-2.2.25+/Bin/Blastn: No Such File Or....
Hello, I want to set a local blast in my system..but it showing some error while i am working. I have set Environment var path /home/abc/ncbi-blast-2.2.25+/bin in .bashrc file. i also have set the...
View ArticleUse Megan To Parse Sam File
Dear all, I got a question about using MEGAN4 to parsing SAM file. What I want to do is to get taxonomic and functional annotaion of my raw reads against nr database . As the raw reads is too big (11...
View ArticleMaking Specialised A Local Blast Db
Hi,I need to make a local Blast DNA (nt) database that only includes sequences from plants. I'd also like to make one with only chloroplast sequences. Put I can't find any tools to do this. I don't...
View ArticleDefault Ncbi Blast+ V. 2.2.25 Parameters
Hi:I'd like to compare my own BLAST tool with NCBI blast+ tool but couldn't find the default parameter of this version. I'd like to know the scoring scheme for match, mismatch, opening gap and extended...
View ArticleRpsblast And Formatrpsdb Problems
I'm trying to install the CDD database locally using rpsblast. However, I've run into several problems. I can't seem to find formatrpsdb after compiling BLAST 2.2.24 from source. Has it been replaced...
View Article