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 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 ArticleHow To Define And Calculate Cip ( A New Parameters For Blast Analysis Of Cip...
IN the paper “Improved criteria and comparative genomics tool provide new insights into grass paleogenomics " they said:To increase the significance of inter-specific sequence alignments for inferring...
View ArticleHow To Make Pssm With Makeblastdb
i want to make a pssm from a fasta file for searching with rpsblast, i have the 2.2.23+ version of blast, so formatdb is replaced with makeblastdb. I have used it to make a database from the genome im...
View ArticleNcbi Legacy Blast Usage With Tblastn/Pssm
I'm trying to get a webservice for protein discovery running. I would like to perform a tblastn with a PSSM from NCBI's archive (smp file). This works fine with NCBI BLAST+, but unfortunately the...
View ArticleCreating A Dna Sequence Database Locally For Blastplus
Hi, I have a fasta file containing cDNA sequences and I would like to create a blastable database for blastplus, (using blastn) that I have installed locally. I am, however, unsuccessful up to now as I...
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][1], cave LARGE file). My database is containing nucleotide sequences and 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 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 ArticleKegg Mapping-What Does The Colour On The Pathway Means?
Hi all, I am doing transcriptome analysis and i have just performed GO-KEGG mapping with blast2go v2.4.2. The results contain maps with EC of multiple colour. Do any one know what all these colour...
View ArticleHelp With Formatdb And Blast All
I have my own database of sequences stored in MySQL. I convert this database into a blastable format using formatdb, code below: formatdb -p T -i db.fasta I then do the same with the query sequence and...
View ArticleGet Pairwise Sequence Identity
Hey,for some project I need to run pairwise sequence alignments (local ones, i.e. Smith-Waterman) on protein sequences in order to produce a similarity matrix based on the percentage of identical...
View ArticleBlastp And Biopython
I have noticed that when I blast my own database in particular some of the sequences get truncated. This is using my local blast algorithm. For example I know that the sequence `FYNTSTPQ` and...
View ArticleAnnotating Sequences For Gbrowse - Which Is The Database And Which Is The Query?
Let's say I have some small sequences that I wish to display in Gbrowse. I want to create tracks from Blast results to show where genic regions might be.Do I create a Blast index of the small sequences...
View ArticleRun A Blast Daemon
I want to run my own BLAST daemon to avoid loading my blast db into RAM for every query.When I google it: I get a page from IBM that is out-of-date and a lot of other pages about Buffy the Vampire...
View ArticleCustom Matrices With Ncbi Blast
Does anyone have an idea on how to make NCBI BLAST work with custom Matrices? i.e. ones that are not provided by the BLOSUM series that come as a default with NCBI BLAST.
View ArticleCompare Two Protein Sequences Using Local Blast
Hi,I have been given a task to compare the all the protein sequences of a strain of campylobacter with a strain of E.coli. I would like to do this locally using Biopython and the inbuilt Blast tools....
View ArticleHow To Convert Blast Results To Gff
I'd like to visualise the results of a BLAST search in a genome browser. Is there a simple way to get the results in GFF format without having to write a parser myself?
View ArticleMerging Blastx Hits From Overlapping Bacterial Genome Segments
I blastx-ed 1Mbp bacterial genome fragment against NCBI nr database. I have split it into 2000bp fragments with 500bp overlap into a one multiple fasta file (splitter from EMBOSS) splitter -sequence...
View ArticleTaxonomy Of Blast Hits
Lets have 200k genomic contigs with some (unknown) bacterial contamination. I blasted (blastn vs nr) all of them, got tabulated output and passed the uniq acc nos ca 5k to Batch Entrez. Since neither...
View Articlecarboxylesterases classification into subfamilies
Hi! I want to classify the carboxylesterases genes into subfamilies. There are about 17 subfamilies for these gene, but it is varying a lots in different species. so it is hard to find reference...
View ArticleAre there any online/offline internships in bioinformatics? Stipend does not...
Are there any online/offline internships in bioinformatics? Stipend does not matter. I'll be able to invest 2 hours per day. (I can’t give it more time than that because I have some competitive exams...
View ArticleBiopython Ncbistandalone Blastall Gives Different Result Than Calling...
So, first I tested what results I should get from the blastall program using the command line, with e-value 0.001: C:\Niek\Test\blast-2.2.17\bin\blastall -p blastp -d...
View ArticleHow To Show More Blast Results Using Biopython?
Hi,I'm using biopython to BLAST over the internet. However, it only saves 30 results (there are more than 30 results that are under the e-value I chose) in the xml. I've been looking all over but can't...
View ArticleBlastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access...
When I run blastn (version 2.15) and nt database (latest version) was extracted. I used aspera to download database from ncbi This is code I used to download database: ascp -T -i...
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