Running Blast With C
I'm trying to improve the parallelization of something and it is beneficial to not use system calls to start blast runs. It seems NCBI only has documentation for doing this in a C++ environment, but...
View ArticleComparing Bowtie H_Sapiens_Asm Blastn -Task Blastn-Short -Db Human_Genomic
I am thinking the current supplied (pre-formatted) blastn humangenomic database from NCBI contains many many duplications of the same sequences. Is this correct? I think I only need the current...
View ArticleQuick Command To Split Large Blastx Files?
Any thoughts? I have large 7 gb files as resulted from Blastx any clue how to split them?Edit:These are standard blastX files (fasta). I need to split them for a program (binning) call SOrt-ITEMS/MEGAN
View ArticleFinding Pdb Codes Of Sequences Homologous To An Input Sequences
I need to write a script that can do a blastp with an input xml file, then find and display the PDB codes of sequences that are homologous. The definition I'm using for homology is: 1. the HSP in the...
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 ArticleBlast Results: Xml Tags Explained ?
Hi there,I would like to know if there is any description of the tags that are found in the XML file generated by blastall. I just cannot find any comprehensive document on the web .More precisely, I...
View ArticleHow To Get Ungapped Sequences From Blast Output?
I am interested in getting ungapped sequence hits (hspsnogap) from blast output, I tried using this:result_handle = NCBIWWW.qblast("blastp", "nr", record.format("fasta"),expect=10,"hsps_no_gap")...
View ArticleBlast Nucleotide Vs. Nucleotide, Plus-Minus Results Only
Hi Folks, I am interested in running a blastn search to search for complementary sequence (potential biological function) between two groups of sequences, (Query blasted against Reference) such that...
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 ArticleBlast/Reblast To Verify Homologies
Hi!I am an informatics student from Germany attending a practical course on bioinformatics. I am new to the field of bioinformatics but I am willing to learn a lot. My first task is the following: I...
View ArticleStandalone Blast Issue
Dear all,I have recently installed blast-2.2.26 on my machine (running MacOS 10.7.3) and I tried to perform a BLAST search using a single protein sequence as query and a formatted (by me) database...
View Articleblast against genomes in biopython
from Bio import Entrez, SeqIO from Bio.Blast import NCBIXML from Bio.Blast import NCBIWWW result_handle = NCBIWWW.qblast("blastn","nr",...
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 ArticleBlast more thn several DNA sequences
Can we blast several DNA sequences against whole genome simultaneously? If yes, thn How?
View ArticleBlast output query
I did a local standalone blast pre-miRNAs against a genome in tabular format (-m 8) and got the results. My next steps for refining the results include GC content analysis, RepeatMasker etc. I am...
View ArticleBlast Multifasta Against Ncbi Nr Database, And Download All The Results
Hello, i have a fasta file with 7600 nucleotide sequences, i have a local nr database formated for blast, with makeblastdb, i don't use formatdb because it give errors (zero length sequences). I blast...
View Articlencbi-blast+ ThrowNullPointerException() when running inside a Docker container
NCBI blast+ seems to have trouble parsing some fasta files when running inside a Docker container. Note that I don't see the error when running blast outside the container. I'm using the sample input...
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 ArticleWhy is pre formatted refseq database larger than nt database in blastdb?
I went to the blast ftp database ftp://ftp.ncbi.nlm.nih.gov/blast/db/, there are 18 nt files, each is less than 800 MB, and for refseq_genome it has 83 files, most of which are larger than 800 MB,...
View ArticleNcbi Refseq Viral Genomes
I want to create custom blastdb with all viruses available in the refseq. But I don't know which source files to use. My first point is:ftp://ftp.ncbi.nih.gov/genomes/Viruses/From research I concluded...
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