Exact Matching With Bowtie, Blat And Blast+
I am running bowtie with the following parameters, to look for up to, say, 10 exact matches of a 36-base nucleotide string to a GRCh37/hg19 index, _e.g._: $ bowtie -S hg19 -v 0 -k 10 -f sequence.fa...
View ArticleSetting Up Blast Server
Hi, i'm trying to set up my own blast server for convenience and i'm having some technical issues which might not be purely bioinformatics related but i hope someone here has done it before.My problem...
View ArticleTrouble With Local Psiblast
Hello everyone,My requirement is to generate a PSSM (Position Specific Scoring Matrix) from a given protein fasta sequence against a protein database. I have downloaded and installed the latest version...
View ArticleTrying To Run Psipred But Failing To Use Blastpgp
Hi - I am trying to run psipred (http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/) and it requires blast+ to be installed. I have done this, and all the blast executables are stored in...
View ArticleA Tool For Flagging Blast Searches?
I want to know if there is a blast way or a blast-like tool in which a query will search through a database and return only predetermined hits based on given flags like sequence fasta ids. To be more...
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 ArticlePerl Script For Blast+
Hi, how can I blast using perl script as I have whole database i.e subject with me and a single protein file is arranged in FASTA format. I have used Blast+ for the creation of database and have three...
View ArticleGetting Taxonomic Blast Table Output Of 2.2.28 Using A Local Copy Of Nt
Hello!I understand that taxonomic information for each blast HSP can now be output in the blast custom table format new in blast+ 2.2.28. My simple question is: how do I set up a local copy of NCBI's...
View ArticleRunning Blast For A List Of Pairs
Hi,I would like to ask if it is possible that I run BLAST with a list of pairs of query and reference sequence IDs?I tried bl2seq but unfortunately it does not produce the alignment of the whole...
View ArticleAnalyzing Overlap Of Results Between Blast Queries. Is There A Tool For This?...
I am using various set of enzymes organized into classes in my research. As part of this I use PSI-BLAST to increase the size of my data sets. I known there is a large amount of overlap returned in the...
View ArticleLimit The Memory Size Of Blast?
Would anyone tell me whether it is possible to limit the memory size in blast+/blastall search? If possible, how should we do it? Thanks!
View ArticleBioperl Standaloneblastplus, Cleaning Up Thousands Of Temp Files
Hi, I'm using StandAloneBlastPlus BioPerl module as NCBI blast+ wrapper. I have to perform sequence alignments against a database of bacteria using multiple processes on a cluster. A temp file (.fas)...
View ArticleForum: How To Correctly Speed Up Blast Using Num_Threads
Hello, I did a short blast comparison using multiple cores to see how they behave. I published it in my blog and thought it would be a good idea to share it...
View ArticleFastest Way To Search For Perfect Matches Only In Blast Or Blat
Hi, I have a numerous 100-mer sequences (let's say billions). What I am going to do is to query these sequences to entire human genome to find "perfect matches" only.I first tried to do this using...
View ArticleWhy Do I Get A Makeblastdb Error: File Does Not Match Input Format Type,...
hello guys after giving the following command i am facing error for the output file being generated....However formatdb was able to accept my FASTA file and i was successfully able to run my blastn on...
View ArticleHow Can I Record A Specific Domain Sequence Within A Protein Query?
Hello everyone: I'm just beginning with massive search on my own database of proteins and I need some guidelines to start. What I'm trying to do is recording (as *.fasta file) a specific domain...
View ArticleBlast+ Nucleotide "-Matrix" Command
HI, I've been trying to run a nucleotide blast (blastn) using BLAST+ here is what it should look like using legacy blast: blastall -p blastn -d db -i fasta.fasta -o output.blastn -e 10000 -F F -a 7 -M...
View ArticleIn Blast+, How Can I Ignore The *** No Hits Found *** In Output
Hi,Doing a blast+, using the default output ( -outfmt 0 ), there is a way to not save all the queries that doesn't hit ? I want to eliminate from output the lines around No hits found , I think it's...
View ArticleBlast+: Error Messege
I want to convert 16S Microbial pre-formatted database in fasta format. I use Blast+ program (2.2.27+ version Window). I could install this program and I know that I must to use blastdbcmd command. The...
View ArticleBlastclust Has Been Depreciated. Does Anyone Know Why?
I am working on machine learning project using SVMs. One of the steps in the preparation of my data sets is to reduce the sequence similarity in each class to 40%. I have compared CD-HIT and BLASTCLUST...
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