Are Alignment Lengths Reported In Ncbi Blast+ Results Counting Nucleotides Or...
Very simply, what are the units of the alignment length reported by BLASTX and BLASTP? The units of length are not listed in the output column headings (-outfmt 7) and I have found nothing in the...
View ArticleCan You Explain The Differences Among These Blast Databases?
I am trying to blast my sequence against primate databases remotely. But there are so many databases, and most are in abbreviation. Can you explain what they are in the below example list? chimp AACZ...
View ArticleAssigning subject to query based on coverage from blast output file
Dear all, I have blast result in tabulated format. Each of the query hits multiple subject sequences. From all of those hits, I want to assign that subject sequence which covers the query sequence the...
View ArticleHelp With Rps-Blast With New Blast
HiI want to make rpsblast with the new blast 2.2.25 with rpstblastn. But I need to format the database. I think for the older blast version you use formatrpsdb and it´s create others files including...
View ArticleFind Mismatch And Gap Positions
Hi everyone,I want to find the homologs of many short sequences, and then identify the mismatch and gap positions for each pair. The first step can be easily done by BLAST, FASTA or patscan, but the...
View ArticleHow To Convert Db Format From Nih Blast To Blat Requirement
Hi I want to run a local BLAT for a huge set of short reads and intend to use BLAT for that. I find that the env_nt db from NCBI is in a different format whereas BLAT requires .fa, .nib or .2bit files...
View ArticleFrom Sequence To Gene Id
Hi,I have around 10000 fish EST sequences in a fasta file and want to have an Entrez gene ID for as many as possible of these sequences. The reason I want Entrez gene IDs is to facilitate gene ontology...
View ArticleUsing Blast2Go From The Command Line
Hi,I am looking for a way of using Blast2Go on a remote server in a more or less FIRE AND FORGET manner. My idea is to use either a command line version of Blast2Go or an API that would permit me to...
View ArticleDna Sequencers- Required Matching Errors For 150 Bps
I am doing some experiment using BowTie and WHAM which are short read aligners that aligns short DNA sequences (reads) to the human genome like BLAST. In WHAM, it is specified that for 75 bps reads, it...
View ArticleBest Blast Hit Without Pain
Hi,This might be naive but here I go. I have a set of target sequences and a query sequence. I want to find the best BLAST hit (lets say using the bit score). The straightforward way to do this is to...
View ArticleConvert Blast Output Into Blast-Xml
Hey!Problem: I need to convert a standard Blast report into the blastxml format.Background: For speed reasons, I am using UBlast (Usearch) instead of NCBI-Blast. UBlast outputs either tab-delimited...
View ArticleProblems With Blast And Nr Database
I'm familiar with the BLAST family of software: I've used both the old interface (blastall, formatdb, et al) and the new interface (blastx, makeblastdb, et al). However, I've always used it with...
View Articleerror downloading refseq for local BLAST install via FTP
I am having trouble downloading the refseq database required for BLAST+. I am following the instructions from http://www.ncbi.nlm.nih.gov/books/NBK52640/ but get No such file or Directory error using...
View ArticleBlast: Homology Or Similarity?
Hi Biostars, I am having a dispute with a reviewer. Is BLAST a Homology or similarity based search? thanks EDIT The BLAST is performed against a custom DB containing only homologous proteins.
View ArticleTaking Only Aligned Sequences In A Blast
Hello,I would like to know how to take (in FASTA format) only the sequences displayed as results of a BLAST, avoiding to search the desired sequences in the whole subjects' reports.
View ArticleBlast Can'T Find Databases
I've installed BLAST locally, I've downloaded the nr database via update update_blastdb, I've added .ncbirc to the home folder which has [BLAST] BLASTDB=/home/bioinformatics/Desktop/blastDBand yet when...
View ArticleSEED assignment (MEGAN5)
For me it is not clear how MEGAN assign the SEED classes to the sequences. In the manual, it says that it is made throughtout the identification of RefSeq id (accession number?). When I load my blast...
View ArticleError Using Makeblastdb
Hi there,I am trying to run makebastdb to create a new BLAST database. The program starts but cuts out abruptly with an Error:Error: ncbi::s_FixBioseqDeltas() - Bioseq must have Seq-data or Delta...
View ArticleHow To Get Fasta Source File From Blast Csv Format?
I am currently writing a library that uses the -outfmt 10 option of Blast, which give you a CSV instead of the pretty human readable format.Liketblastn -db dmel_a -query somequery.faa -outfmt 10The...
View ArticleStarting Point
I am trying to get into bioinformatics or just trying to get a jist of what is going on. I wanted to see the difference between different methods for gene variation. I looked at blast and installed it...
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