Create 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 ArticleRetrieving Results Using Blast Soap Api
Hi ; I have a problem with using Blast SOAP API. Previously, I used the downloadable version of blast in which I balstp against PDB using the following command line:"blasp.exe -query input.txt -db...
View ArticleHow to do automated blast with mulitple sequences and BLAST each one...
Is there an automated program that can take mulitple sequences and BLAST each one individually???
View ArticlePsiblast: Stop After Checkpoint?
Hi,I'm using psiblast 2.2.25+ to generate PSSMs for PSIPred, and I noticed that even after writing to the checkpoint file, it takes a while (feels like half the run time) before exiting, even though I...
View ArticleHuman Genbank Ids
I am working on a sequencing run that contains contamination. I did a de novo assembly and blasted the results against NR and filtered for the best hits. I now have a list of Genbank Ids. I simply want...
View ArticleForum: Sequenceserver: Easily Deploy A Custom, User-Friendly Blast Webserver
Executive Summary: SequenceServer lets you rapidly set up a custom BLAST+ server with an intuitive user interface for use locally or over the web.Why we created it: We were frustrated with:too many...
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 Could I Run A Huge Number Of Blast Calls Faster?
For the purpose of my project I need to break down a genome and run blast for each part. Because of the amount of genome file it would be at least 4000 call of blast which would take a lot of time. I'm...
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 ArticleScientific Names In Blast Output And Databases
Hi, I'm interested in getting the scientific names of my blast hits ran locally. I see blast+ search apps have option -outfmt which can take sscinames(seems new in version Blast+ 2.2.28), but even...
View ArticleBlastn And Blastcmd Issues - Blast
Hey all, first of all I'd just to say that I am fairly new to the field of bioinformatics and I'm, unfortunately, learning by my mistakes more than my successes atm and I'm having some trouble...
View ArticleHow To Generate Blast Database
Hello I downloaded some database in gemnomes/Bacteria ( ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Acetobacterium_woodii_DSM_1030_uid88073/ ) I want to use blast program. I have some problem. How can...
View ArticleIdentification Of Promoters From Gene Sequences And A Vertebrate Genome Assembly
I have a number of genes which I'd like to locate in a whole-genome assembly, in order to identify the genes' promoters. In the past I've done this manually using BLAST and BLAT, which has worked well,...
View ArticleStandalone BLAST with kingdom classification
Hi all,I have an assembled transcriptome from an organism hosting various symbionts and I'm now interested in how many of my contigs hitting to the different kingdoms. What I've found so far is the...
View ArticleWhat Is The Lowest E-Value In Blast When Ncbi Rounds It Down To 0 (Zero)?
Hello, Just out of curiosity, an E-value of more significant hits in BLAST approach 0, but cannot equal 0. In some cases when the E-value of a HSP is very low NCBI BLAST rounds it down to 0. What is...
View ArticleBlast 2.2.24+ Database Error
When running local BLAST on a big database (all human proteins) I get the following error:proteinsApplicationError: Command 'blast-2.2.24+/bin/blastp.exe -query "query.fasta" - db...
View ArticleRaw Alignment Score Calculation
Thanks for lots of answers and I've started with lots of sources here. It helps me to get a good introduction to blast.After I've now a little more understanding I can ask more specific questions such...
View ArticleHow to recreate alignment information from TSV output
Hi,I have obtained BLAST output file in TSV file format which looks like - # BLASTN 2.2.29+ # Query: SI2.2.0_06267 Si_gnF.scaffold02592[1282609..1284114].pep_2 # Database:...
View ArticleComputing The Bit Score, E-Value And P-Values In Blast
Hello, I'm having some trouble with calcualting the following things; Bit score E-valueP-value I know the formulas, but I just don't know how to apply them to the following sequence:...
View ArticleConverting Blast Results In Fasta Format
Hi, I "blast" my protein sequence against the NCBI database and I wish to save the returned results in FASTA format. Is there a way to convert the sequences all into FASTA format and save them or do I...
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