getting error in runing tblastn
Hello group, i am trying to run tblastn of version 2.2.26+ for mapping peptides on eukaryotic genome, i am running the command tblastn -query sequence.fa -out output.txt -subject ref_protein.fa -evalue...
View ArticleBlast The Sequences Obtained From Translocations To Get Their Positions
HI I have a file that contains information like this:Gene1 Gene2 sequence FOXP1 ABL1 acacctctcaatgcagctttacagCtctacgtctcctccgagagccgctgtggagagttacgtcgaaatgtc FUS ATF1...
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 ArticleMegablast, Makembindex, And Choosing Nmers
I've been using MegaBLAST (in BLAST+) to test for high-similarity matches against hg18. It's exponentially faster than normal blastn for this purpose, but I'm not sure what settings I should use when...
View ArticleHow To Produce An Analysis Report From Blast Output ?
Hello, is there a tool for processing the blast output and perform a statistical analysis of the alignment? For example a plot of the position of the mismatches? I cant believe that there is no...
View ArticleHow To Identify Proteins Present Only In Pathogens But Not In Non-Pathogens...
I used PSI-CD-HIT-2D to compare the proteome of pathogen A to pathogen B from the same genus at 30% identity. The matched protein sequences (homologs above 30% identity) are then compared again to...
View ArticleImport Xml Blastx Results In Geneious
Hi,I have the xml results file of my local blastx and I would like to import the annotations directly on my sequence in geneious. Do you know if there is a way ?Thanks,Aurelien
View ArticleExtracting Query Sequence From Blast Xml Output Using Ncbixml Parser
I want to Blast my data base of sequence (Aminoacid) with a data base. And get sequences which have a given score and e value less than 0.5 . So I ran blast with e-value 0.5 and now i want to isolate...
View ArticleRunning Blast On Amazon'S Elastic Mapreduce
Hello, I need to extract 10 million (yes, 10 million) sequences from the blast database -nt using the blastdbcmd command. Needless to say this will take days on my rinky-dink desktop ( In an earlier I...
View ArticleHow Can I Download The Results From An Ncbi Blast Search?
I'm BLASTing a sequence on NCBI (http://blast.ncbi.nlm.nih.gov/Blast.cgi#), I see a page of results showing the portions of the sequences that aligned to my search sequence. I now want to download...
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 ArticleProcess tabular BLAST output
Dear all,Iam struggling with processing tabular BLAST output. I would like to do the following:Take a Blast output table (simplified):Sequence ID | e-value | GISeq1 0.001 12345Seq1 0.001...
View ArticleLocal Blast: Querying A Single Sequence Without Input File. Possible ?
Hi,When using BLASTALL by command line, is there any way of querying BLASTALL without using any input file but a directly a sequence ?I would like to do something like:blastall -n blastn -d MyBud.fna...
View ArticleGenerating Protein Consensus Sequence For Blast Input
I have a set of 3 protein sequences for which I need to find the "consensus sequence" which can be used as an input to blast against a local database.how should I go about it?
View ArticleBlast Alignment Bug
I tried to find a short oligonucleotide sequence (probe) in a transcript and I knew for sure that the transcript contained the probe. But the latest version of the BLAST stand-alone algorithm (2.2.25+)...
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 ArticleProblem Parsing Xml In Biopython
Hi mates, I m new in python and I m trying to parse a result from local Blast...here the code.from Bio.Blast.Applications import NcbiblastpCommandline from Bio.Blast import NCBIStandalone from...
View ArticleBlast Results: Xml Tags Explained ?
Hi there,I would like to know if there is any description of the tags that are found in the XML file generated by blastall. I just cannot find any comprehensive document on the web .More precisely, I...
View Articleblastn -no_greedy switch
Does setting the -no_greedy switch make blastn behave like Smith-Waterman? The documentation states that the switch allows blast to "use non-greedy dynamic programming extension". It isn't clear to me...
View ArticleHow To Scale A Pssm For Ncbi Blast
Hi again,I'm trying to do a local NCBI BLAST search using the PSSM of a conserved CDD domain (.smp file in the database, cave LARGE file).My database is containing nucleotide sequences and the PSSM is...
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