How To Find Sequences With A Given Number Of Mismatches
Hi! Is there any script or tool that allows to find similar sequences given the maximum acceptable number of mismatches? What I want is something similar to a Blastn search, but instead of filtering...
View ArticleFrom Blast To Ucsc Genome Browser: Valid Loci
Hello,BLAST, sometimes, does not propose direct links to Genbank pages as reports, and this leads to unaccepted entries in the UCSC Genome Browser's search term box. How could I avoid those results? Is...
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...
View ArticleNcbi C++ Exception: Ncbi::Cmemoryfilesegment::Cmemoryfilesegment() - File...
I have tried running a command line blast. The query file is a multi fasta file containing 2600 sequences. It was made a BLASTX against a proteins sequences (ProDom) of size 2 GB (prodom.phr : 1:00 GB,...
View ArticleFASTA-Reader: First data line in seq is about 100% ambiguous nucleotides...
I am not sure if this is a problem or if in fact the process is correct. Any help is much appreciated. I am trying to make blast databases from assembly fasta files, and have seeing the above error. It...
View ArticleGet Pairwise Sequence Identity
Hey,for some project I need to run pairwise sequence alignments (local ones, i.e. Smith-Waterman) on protein sequences in order to produce a similarity matrix based on the percentage of identical...
View ArticleAny tool to generate protein similarity matrix
Hi, I want to calculate the similarities between each protein pariwise and then implement random walk to predict interactions. A paper mentions "J. Mol. Biol. (1981) 147, 195-197" to compare two...
View ArticleBlastdbcheck Error
I keep getting errors on the following command:blastdbcheck -db nt.00Writing messages to <stdout> at verbosity (Summary) ISAM testing is ENABLED. Legacy testing is DISABLED. By default, testing...
View Articleshort protein BLAST
Dear AllI am performing BLAST. The database is a collection of short protein sequences (~40 aa in length, short but not short very much). The query file contains short protein sequences as well (~40...
View ArticleE Values Using Blastp In Biopython
Is there a reason for the E Value to differ when using BLAST on the web and using BioPython? My understanding is that these are the same source, so I am unable to understand the following differences....
View ArticleFind The Rid For A Remote Blast+ Result
I ran a remote blastn search using the command line blast 2.2.25+ and got the results back in asn format. when I went to reformat the results using blast_formatter, I realized I needed the RID for my...
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 ArticleProtein Sequence Homology Score, Align Or Blast
Hi,I want to get homology scores for every pair of human proteins acoording to their sequence amino acid constitution. should I blast these pairs(blast2seq) or align these pairs(localAlignment)?
View ArticleDownload Ensembl Blastn Result
Hi,How can I download blast results from ensembl. I blast 10 sequences against all ensembl species. Now I have the result page and I want to download all hits to compare them.Is it possible ?Here's the...
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 ArticleAverage nucleotide identity
Hi,I'm using ANI to determine if two bacteria species are related or not. What is the threshold for saying two sequences come from different species ?
View ArticleProblem Parsing Xml In Biopython
Hi mates, I m new in python and I m trying to parse a result from local Blast...here the code.from Bio.Blast.Applications import NcbiblastpCommandline from Bio.Blast import NCBIStandalone from...
View ArticleHow To Generate A Species Distribution From Blast Xml Output
Hi,I am very new in bioinformatics field. I have a BLAST XML output file and I need to parse it to generate a species distribution. I was hoping someone could show me how it can be done by Biopython...
View ArticleBlast RNA nucleotide sequences with Protein-RNA complexes
Hi,I have two datasets - one folder containing nucleotide sequences of different only RNA proteins and the other folder containing different protein-RNA complexes (all FASTA files). I want to blast...
View ArticleImport Xml Blastx Results In Geneious
Hi,I have the xml results file of my local blastx and I would like to import the annotations directly on my sequence in geneious. Do you know if there is a way ?Thanks,Aurelien
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