Error 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 ArticleIs It Possible To Get Near Global Alignment From Blast?
Hi to all When a query sequence identical to a database sequence is done BLAST, the alignment is shown for 100% of the sequence ie.complete coverage. Cannot this situation may be said global alignment?...
View ArticleE-Value In Blast
Hi all:I am calculating my e-Value for my own BLAST alignment. I used the formulae: e= mn2^-S'where: m = length of the query sequence n = total number of lengths of all template sequences in the...
View ArticleHow To Convert Db Format From Nih Blast To Blat Requirement
Hi I want to run a local BLAT for a huge set of short reads and intend to use BLAT for that. I find that the env_nt db from NCBI is in a different format whereas BLAT requires .fa, .nib or .2bit files...
View ArticleTurn Off Blast Search On Reverse Complement Strand In Blastn
I have a quick question: How can I turn off search on reverse complement strand of my query nucleotide sequence in blastn?For example, I don't want 'GUAAAGCCAAAUCUUCGGUUA' to be a hit when I use...
View ArticleGene Function through sequence homology
HiSo I've got list of genes putatively involved in Leptospira virulence, and I want to produce hypotheses on their function through sequence homology. So I was thinking of BLASTing them as a first...
View ArticleProblems With Biopython When Running The Ncbistandalone.Py Program
Hi, I am having problem while running NCBIStandalone library of biopython. i want to retrieve sequence titles from output of blast but it gives error on iterator. Following is the code to retrieve...
View Articlequery on micro RNAs(miRNAs)
Hi community,Actually i am new to bio-informatics. i am working on insilico mining of miRNAs. in one article it was given that n/n, n-1/n and n-2/n nucleotide matches, whereas n represents known miRNA...
View ArticleMakeblastdb Error
I ran into the following error when trying to build a database using makeblastdb (NCBI BLAST 2.2.23+).> makeblastdb -in uniprot90.faa -dbtype prot -parse_seqids Building a new DB, current time:...
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 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 ArticleHow To Make A Blast Database With Taxonids From Ncbi Query.
I am seemingly stuck with something that should be very simple and I hope I haven't overlooked something obvious. Question: How can I make a valid Blast-database with Taxids from a NCBI query export?...
View ArticleHelp With Rps-Blast With New Blast
HiI want to make rpsblast with the new blast 2.2.25 with rpstblastn. But I need to format the database. I think for the older blast version you use formatrpsdb and it´s create others files including...
View ArticleBlast Results Wont Return
This isnt my usual way if doing things but because im using Plone it has to be done this way. The function below takes a variable "x" which is the query sequence. Its is then formatted to a blast-able...
View ArticleBLASTP many pairs of peptide sequences
Dear all,I have many pairs of protein sequences, an example shown below.MDDDIAALVVDNGSGMCKAG DDDIAALVDNSGSMCKAGTTAEREIVRDIKEKLCY TTAEIVRKEKLCYVARMQKEITAPSTMKIKI KEITALPSTMKIKII... ...I need to...
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 ArticleChanging evalue doesn't change the results of blast
Hi! First's run results occurred by this command : tblastn -query query.fasta -db plant_DB -out output-evalue -html and in some reads i got two targets. e.g : Score = 160 bits (404), Expect = 1e-44,...
View ArticleCreate a custom .gtf file with a list of genes
Hi GuysI am new to the RNA Seq world and just starting out with linux. I need to create a custom gene annotation file with a list of genes I am interested in analyzing. How do I do that.
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 ArticleHow Scores are given in Substitution matrix like PAM and BLOSUM?
hi everyone..while aligning two protein sequences, amino acid of the query sequence n amino acid of Database sequence is aligned..if both match a score is given..if there is a substitution of aminoacid...
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