PhD student in University of Valladolid
The regression of water potential values with various parameters of grapevine such as yield, vigour is positive, to mean that as the water stress level decreases to more low (high stress) these...
View ArticleFormatdb problem in Unus package
I´m using Unus, which is Perl package for phylogenomic analyses. In this package, the blast-2.2.25 is used because the package uses the formatdb program, as follows:if(($self->{'program'} eq...
View ArticleIs there a succinct method of isolating sequences phylogenetically similar to...
This is a bit outside of my wheelhouse so I apologize if some terminology is incorrect.I have a number of reference RBCL gene sequences for a taxonomic family, and I want to extract sequences from a...
View ArticleBlast A Specific Contig Against Multiple Contigs From Another Organism
I have a contig from one organism that is of interest. I have been searching this contig against another organisms complete collection of contigs found on NCBI by using an online DNA translator and...
View ArticleCan Biopython Parse Gzipped Xml From Blast?
I have been using blast+ with the xml output format (-m7 in the older days, and outfmt 5 with ncbi-blast+). Since the XML files are huge, I have been gzipping them. I have also been using Biopython to...
View ArticleBlast a gene against one genome
Hello,I want to run a blast of one gene against one genome. I have a fasta file of them both. Is there any way to run it other than converting the genome to a DB file?Thank you in advance
View Articlemakeblastdb with FASTA file error: "does not match input format type"
Hi all - I have been trying to set up a local database with the Drosophila melanogaster genome to use with Blast+ and have been having a lot of trouble. I tried using makeblastdb as follows:makeblastdb...
View ArticleSpecies-Specific Output From Blast -Db Nt -Remote ...
I'm using the C++ version of blastn, with -db nt and -remote. I need to limit my search to a specific organism. I've had success using -gilist <file> to do this on searches with a local database,...
View ArticleComparing Blast M8 Outputs
Hi,I want to compare BLAST outputs in m8 format to find out if any queries in the separate output files have the same subject hits to NCBI nr database.For example, for the 2 BLAST outputs in m8 format...
View ArticleHow Set A Pssm (Position Specific Scoring Matrix) When Querying With Blast+?
help me out if anyone knows the answer for my question, How to search a nucleotide database using PSSM ( i developed the PSSM using set of protein sequences from query set) Do provide me the command in...
View ArticleCreating An Rpsblast Database From An Hmm Profile Library
I have downloaded the HMM library file from CATH and would like to convert it to a rpsblast database.Therefor, I think I need to do the following steps:Extract the HMM profiles from the library (this...
View ArticleBlastn - Program Runs Indefinitely When Generating Xml Formatted Output
I am running blastn on some nucleotide data, and it seems to run indefinitely when I generate XML output. The jobs take ~15 minutes when generating either the default format or tab delimited, but when...
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 Articledownloading a Mus musculus genes dataset from ensembl biomart
iam been trying to download a dataset of mus musculus gene coding regions from biomart, ensembl to serve as reference to my query sewuencesthe problem is that no matter how many times i try the file is...
View ArticleHow to analyze the ProDom output? I have some results to support the...
Hi all, I have some results retrieved from ProDom database and I need to analyze the output from 3 inputs to check if they share the same conserved domains, the results points to same description of...
View ArticleAbout Blast Scores In Matrix Format.
Hi All, How Can I get local Blast score in matrix format??( I have score but I need in Matrix format) How can I run blast of 200 sequences in order to alignment sequences by writing a python...
View ArticleBlast Error: Tax database file not found
Hello, I am running this command for a blast search.blastx -query Ndiv_cap300.fasta -out Ndiv_run -outfmt 7 -db nr -num_threads 32 -evalue 1e-3 -max_target_seqs 5however I get the following error that...
View ArticleBlast2Go Statistics
HI When I run blast2go I want to receive statistics about how many sequences fit to each category. When I go to statistics in the blast2go I only manage to generate graphs. How can I receive the data...
View ArticleError When Using Makeblastdb On A Large File
Dear All,I have created a stand alone blast on my system, to work with NGS data and it is working fine. However, I have got a sequence file which is about 2400MB, which is two large to create a local...
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...
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