Help 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 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 ArticleThe Meaning Of The E In Blast Output
I have a question that's been floating around in my head for a while, and a colleague recently asked the same thing so I thought I should finally get to the bottom of it.What does the 'e' in the output...
View ArticleAre 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 ArticleProblems Using Formatdb And Fastacmd
Hello!!I am having an extremely difficult time with formatdb and fastcmd from NCBI blast.I am trying to make a db from single mouse chromosome from NCBI using formatdb. Afterwards I try to obtain...
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 ArticleCreate Blast Database From Query Result?
Possible Duplicate:make a custom BLAST library using the output of another blast result Hello, I would like to create a BLAST database using as input a file generated after executing a BLAST query. I...
View Articleblast -F F equivalent in blast+
In legacy blast there is an option -F, which turns on or off filtering. By default filtering is ON and it effects my results a lot, so I turn it off by -F F (false)In blast+ I couldn't figure out the...
View ArticleBlast Database Sequences Length
Hi allI am doing blast queries using genomes as databases. I would like to know if is possible to filter out database sequences by their length. So, if there is a sequence in the database that is...
View ArticleAlmost Nothing Mapped Using Bwa Or Bowtie. But A Lot Of Mapping In Blast
I have pair-ended illumina samples with the read length of 100-150bp. I tried to map them to the reference genome/transcritpome, but almost nothing mapped using BWA or Bowtie.When I blast them to nt...
View ArticleI Use Blastdbcmd Command With Nr Database And It Gives Me The "Not Found...
This is the errorBLAST Database error: No alias or index file found for nucleotide database [nr] in search path [/home/aj3/Desktop/h/database::]what should I do? do I have to use any other commands...
View ArticleBlast Formatdb, Multiple Folders/Directories
I have downloaded viral genomes from the NCBI website I want to use formatdb so I can create a BLAST database of these viral genomes. However, they are present as nearly 300 folders, each containing...
View ArticleObtaining the top matches from blast
Hi,I have downloaded the current version of the stand-alone-blast (ncbi-blast-2.2.29+) and I am trying to use blast (blastn) to find similarity of of a group of nucleotide sequences that I have....
View ArticleHow To Get Status Update In Ncbi Standalone Blast?
For example, I am running standalone Blast+ for thousands of EST sequences with remote (NCBI) server. I am not getting any status message like 15 of 100 sequence is running. Is it possible to get any...
View ArticleBlastx For A Million Metagenomic Sequences
I intend to use a similarity based binning program like MEGAN or SOrt-ITEMS or CARMA for analyzing sequences in my metagenomic data set. For this, I first have to generate a BLASTx output of my...
View ArticleNcbi-Blast+ Version 2.2.23 'Make' Error
I'm getting errors when I run 'make' for rmblast-1.2-ncbi-blast-2.2.23+-src. This is the version of RMBlast modified for use with RepeatMasker from their site. I had no problem installing it in Ubuntu...
View ArticleBlast+ Error Code=12
Something really bizarre is going on. I ran 6 tblastn jobs independently using the following command line entry: tblastn -query blastqueries14920.fasta -out blastqueries14920.fasta.out -db...
View Article[Fastacmd] How To Retrieve Sequence From Blast Db
Let's say I have multifasta with protein sequences having internal IDs (integer)>1234 MGKL...*I build blast db using:formatdb -i infile.fa -pF -n someDBBut then, I'm unable to retrieve sequence from...
View ArticleHow To Merge Contiguous Blast Hsps! (-M 8 Tab)
Hi, guys! I performed blastx (-m 8) using a query file of many sequences, and for each target sequence, the output contains many fragmental hsps of significance, and these hsps have overlap positions...
View ArticleHow To Parse Psiblast Results Using Biopython And Blast-2.2.24+?
I'm trying to run a PSIBlast program which selects certain sequences out at every round before it does the next iteration. For this I need the Round attribute shown in...
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