Does 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 ArticleHow Set A Pssm (Position Specific Scoring Matrix) When Querying With Blast+?
help me out if anyone knows the answer for my question, How to search a nucleotide database using PSSM ( i developed the PSSM using set of protein sequences from query set) Do provide me the command in...
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 ArticleIdentifying Clone Sequence Proteins
When conducting a Large Y2H screen to find potential interactions for the HIV-1 MA protein. A number of the clone sequences identified cannot be ascribed to a protein using preliminary BLAST. Do any...
View ArticleHow To Find Paralogs Using Blast
I am trying to find paralogous genes in a model organism (Arabidopsis). To do that am using blast with the sequence for its own database. The first hit I get is the protein sequence aligned with it...
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...
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 ArticleBlast_Formatter: How To Choose Which Database To Read From?
Hi, I am attempting to use the blast_formatter included with Blast+ 2.2.24 to convert a blast archive file to xml format. However, I get this error message when I run the command:BLAST Database error:...
View ArticleComparing Assemblies
I'm working with two transcriptome assemblies. They're essentially different versions of the same transcriptome, one of them just includes more data and is therefore (presumably) better quality. A...
View ArticleHow to use whole computer cluster power for computation of a single job?
I know the computations by breaking the files and parallelize it in SGE or SLURM. I want to use whole computation power (20 node , 80 cores) for a single job without breaking it. If I just submit it (a...
View ArticleBlast2 Vs Ncbi-Blast+
In my debian testing system I have two blast packages:ncbi-blast+ 2.2.25-7 with homepagehttp://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/and blast2 1:2.2.25.20110713-3 with homepage...
View ArticleFastest Protein Sequence Similarity Search Algorithm
I heard of RapSearch2 which claims to be must faster than blast and HMMER which is as fast as Blast. I am wondering if there is any benchmark of such programs since the RefSeq/TrEMBL sequence database...
View ArticleDownstream Analysis Of Assembled Transcripts (Cufflinks, Trinity)
Are there any good available programs/scripts for analyzing assembled transcripts? I imagine something like a script to blastn, blastx and tblastx each transcript and report the best hit. Something...
View ArticleHow To Use Blast To Find Exact Matches Of Short Sequences?
Hi, I am using tblastn (under blast 2.2.25+) for exact peptide mapping (no gaps). I want to map few peptides (about 6 to 50 AAs in length) to genome. However, as I test a known peptide of 6 AAs,tblastn...
View ArticleMakeblastdb Hash_Index: What For? When To Use?
The makeblastdb program that comes with blast distribution has the hash_index option that states:-hash_index Create index of sequence hash values.What is for? When should I use it?
View ArticleTools Parsing Ncbi Blast -M 7 Xml Output Format?
Hi all,Is there any script or tool which is able to parse NCBI blast xml output (produced with -m 7 option) ?I want a tab delimited file containing the following information: Name of the query sequence...
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 ArticleMultiple Blast Output Formats From 1 Blast Run
Is it possible to generate 2 different output formats (tabular and the default one) by running blastn just once or I have to either1) Run it 2 times - one for each desired output2) Generate the tabular...
View ArticleSpecies-Specific Output From Blast -Db Nt -Remote ...
I'm using the C++ version of blastn, with -db nt and -remote. I need to limit my search to a specific organism. I've had success using -gilist <file> to do this on searches with a local database,...
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...
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