Problem With Blastp Of Biopython: Returned Non-Zero Exit Status 1
I want to do a local BLAST using blastp from the Bio.Blast.Applications. However, when I run it I get a runtime error: returned non-zero exit status 1. According to the manual it is Exit Code Meaning:...
View ArticleBlast Large and small fasta, which to be database and which to be query?
Dear all, say i have a small 16S reference database and a large amplicon fasta and I want to classify the amplicons. If i use blast or usearch, do you think if i make the amplicon file into a blast...
View ArticleBlast Settings For Short Sequences
I'm searching for short sequences in nt. By short, I mean 10-20 bases. When I run blastn, I get no results, regardless of my -evalue settings. Here's the test sequence:>ponzr CGCGGTAAAACACATTTG And...
View ArticleCreating An Rpsblast Database From An Hmm Profile Library
I have downloaded the HMM library file from CATH and would like to convert it to a rpsblast database.Therefor, I think I need to do the following steps:Extract the HMM profiles from the library (this...
View ArticleWays To Quantify Proteome Analysis Via Blast
I'm working on software to allow users to blast an entire proteome against a manually curated database in order to attempt to quantify the composition of that organisms proteins against our database....
View ArticleIs There Such A Way/ Program To Do This...
Hi guys,I followed the Trinity/ RSEM/ EdgeR pipeline and have produced some FPKM spreadsheets for genes and isoforms.I am currently analysing the isoforms:I have 3 sample conditions and I am comparing...
View ArticleIs Blastall Only Using Blast, Not Blast+?
Hi all, is blastall using BLAST but not BLAST+? If no, then how do I check which BLAST (+ or not) it is? Thanks in advance.
View ArticleHow can I batch a blast for more than 200 proteins at the same time?
Hi everone! I'm a student looking for a tool like greengene.uml.edu whare I can batch a blast of 300 proteins at once angainst ncbi proteins data base. Since greengene doesn't work anymore I'm asking...
View ArticleHow To Examine Whether Homology Search Method Used(Blast/Hmmer) Is Feasible...
Hallo...how to one examine whether homology method used is feasible for identification of a particular gene family e.g HSP. Suppose i have identified 550 sequences suspected to be a particular gene...
View ArticleHow To Perform A Blast Search From A Java Application?
Hello everyone,I would like to perform a Blast Search form within a Java application, i.e. I want to submit the query and evaluate the results. I have stumbled upon several jars on the web, but none of...
View ArticleBlastclust Ignores The Multithreading Argument (-A)
I'm trying to run:blastclust -a 48 -p T -d ./uniprot/2011_04/all.fasta -v progressI have 48 cores on the server thus -a 48 argument, but only 100% CPU (1 core) is used.I have Blast2 version 2.2.21...
View ArticleWhat Is Score Bits In Blast?
i want to konw that what does it mean score and bits in local blast output from the following example?'. Score = 38.2 bits (19), Expect = 0.11 Identities = 22/23 (95%) Query: 1 cttaacttcagctacctcgagta...
View ArticleAveraging Blast Results
I'm in a situation where I have two sets of BLAST results, and I'd like to compare them (non-rigorously). What is the best way to average the evalues (or bit score, whichever is easier) of the HSPs in...
View ArticleBlastn On Gpu?
Does anybody has an experience in running blastn (nucleotide sequence search) on GPU? The freely and easily obtainable tools only provide blastp that is for proteins. I need nucleotide search. As the...
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 ArticleStrategizing Blast Result Parsing
I have a set of ~200 known sequences of a particular domain that I want to use to fish out similar sequences from NCBI-NT.As you can imagine, my blast results for this dataset are redundant in the...
View ArticleHow To Use The Recon Package To Identify Repeat Families From Genomic Sequences
I'm trying to learn RECON and am experimenting using chr22. My steps so far, roughly:Make blast database from chr22.faBLAST chr22.fa against its own databaseRun MSPCollect.pl (RECON provided script) to...
View ArticleNcbi Blast Command Line Align Two Sequences
I want to align 2 sequences using ncbi blast command line or bioperl script, I am new to blast and I found out that it compare a sequence to a database but what I need it to compare two sequences like...
View ArticleBlast+ Error
hi，everyone！ I use blast+ to make annotation of RNA-seq data against nr. When I run blast, it always stopped by error. my command line is "blastn -task blastn -query Unigene.fa -db human.rna.fna -out...
View ArticleBlast Execution Problem
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:...
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