Problem using a custom blast database in tblastx
Hello. I tried to create a custom DB for blast. I downloaded fasta files from NCBI from an SRA project and then run this command makeblastdb -dbtype nucl -in sra_data-DB.fasta -input_type fasta -out...
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 ArticleHow Is The Word Score For The Look-Up Table Determined For Blast?
I'm going over some slides about BLAST from an introductory course of bioinformatics. I don't understand how the words for the look-up table are scored. The query sequence is split up in words of 3...
View ArticleBlast Query Against Two Different Taxa
Hi,I have a protein sequence which I first do a blastp against NR database without any limitations. It returns a possible protein family and an organism in the output with a very low E-value (something...
View ArticleExtract Unmapped Reads From Blast
Is there a way to tell blast to output the unmapped reads into a separate file or at least the name of the unmapped sequences?
View ArticleHow To Find 50 Homolgous Sequences But Not So Close Related?
Hi, I'm searching for e.g. 50 sequences in Not redudundat blast database. I want to test program for protein mutation prediction - program tries to estimate if mutation is deleterious or...
View ArticlePipeline Or Tool For Going From Assembled Genome Fasta & Gff Files Directly...
I'm hoping this doesn't come off as a lazy question, but I am wondering if anyone is aware of a tool or pipeline out there that directly takes reference genome (supercontigs, contigs, scaffold, what...
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 ArticleGet Snps, Indels From Biopython Blast Parser
Hi all,Is there a way through the bioPython API to get the list of variants from BLAST alignments?I have done my alignments using standalone BLAST by providing -query and -subject, and the output is...
View ArticleQuery Vs. Target Using Blast2
I'm running blast2 locally using DNA sequences in fasta files. I have one large target and a load of smaller query sequences.Version: 1.2.2.21.20090809-1 (blast2)blast2 -p blastn -r 0 -q -2 -G 2 -E 2...
View ArticleHow To Blast A Fasta File That Is Non-16S
Hello,I have a Illumnia generated fasta file that was created using rpoB sequence data. I am looking to BLAST these sequences in order to find the best 3 hits of what organism I am looking at. I know...
View ArticleCombining stats of multiple BLAST queries
Hi all,I have a FASTA file with let's say following structure:>Query_1 actgacgac....>Query_2 gtacgatcagct...I want to BLAST this FASTA file against a set of databases one by one and combine the...
View ArticlePython Program Accepting Fasta And Blast, Outputting In Xml Then Returning...
Ok. The assignment was to write a program which accepts an input argument of a FASTA file and prints the hit_id of all found sequences using three functions: run_blast (accepting the FASTA and optional...
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+ Subtractive genomics
HelloCan anyone explain how I would find the essential genes in C. difficile by using standalone BLAST+, also if it is then possible to subtract these from the human genome using BLAST+.Thanks
View ArticleHow To Generate A Species Distribution From Blast Xml Output
Hi,I am very new in bioinformatics field. I have a BLAST XML output file and I need to parse it to generate a species distribution. I was hoping someone could show me how it can be done by Biopython...
View ArticleStrange Behaviour Of Bioperl'S Bio::Searchio When Parsing Xml Blast Output
Hello, I've noticed some strange behaviour when parsing BLAST .xml output files (-oufmt 5) using BioPerl's Bio::SearchIO library. I have a simple parser script that looks something like:...
View Articlebioinformatics related problems
hello friendsi have downloaded blast database (rpsd; for conserved domain). but i am unable to us it. so plz can anyone tell me how i can use (untar files of cdd.tar.gz file).thanks:)
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 Article(Determine If Necessary And) How To Realign Blast Results For Arlequin?
I am newbie in bioinformatics, and now trying to learn about alignments, so sorry about the lack of vocabulary. After blasting a sequence, this is my output from a BLASTN... lots of other aligns ......
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