Genomic Sequences For Drosophila In Refseq
Pscan was recommended to do TF enrichment previously. RefSeq (for human, mouse, and drosophila, e.g. NM_000546) in one of the acceptable identifiers. I have a list of genes in a non-model organism, and...
View ArticleHow To Convert Blast Results To Gff
I'd like to visualise the results of a BLAST search in a genome browser. Is there a simple way to get the results in GFF format without having to write a parser myself?
View ArticleBiojava And Blast+
Dear all, i´m currently trying to parse several blast output files in order to show the results in my software. Since i have to carry out many blast searches from time to time, i decided to install the...
View ArticleMakeblastdb And Blastx
Hi, I tested the makeblastdb and blastx but doesn't seem working for me. Can you please check if I did anything wrong?I used 2 fasta sequences (SETREF : testDB.fa) as a reference and a file with...
View ArticleHow To Find 50 Homolgous Sequences But Not So Close Related?
Hi, I'm searching for e.g. 50 sequences in Not redudundat blast database. I want to test program for protein mutation prediction - program tries to estimate if mutation is deleterious or...
View ArticleDisagreement When Computing Contig Alignments With Different Tools.
Hi everybody I need a small suggestion : After assembly of one listeria genome with "Spades" i want to plot reference genome with my contig file. So i am using Mauve and Quast 2.3 to plot . Now i am...
View ArticleCompare Two Protein Sequences Using Blast On Biopython Without Making A File...
Hi guys, I have been trying to do this, but I've got stuck. I know how to blast two sequences using biopython and the standalone Blast, but I make files in order to blast them. I think making files...
View ArticleBlast Illumina Probe Sequence To Get Their Genomic Coordination
Hi all, The annotation file provided by Illumina for RatRef Expression chip is poorly annotated. Since illumina stopped selling these chips they stopped updating their annotation as well. So I am...
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 ArticleWhat command generate blast database from file in all.fna folder?
I downloaded genome of Bacteria, which file name is all.fna.tar.gz from ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/. Next I extract file I got folder all.fna. I want to generate all bacteria...
View ArticleIncomplete Blast Database In Ubuntu
hello all, i am trying to do local blast using this command blastall -p blastn -n T -i query.fasta -d nt.12 -o /blast.outi am doing a "blastn" , "-n T" shows i want to megablast. i have downloaded...
View ArticleRunning Blast On Amazon'S Elastic Mapreduce
Hello, I need to extract 10 million (yes, 10 million) sequences from the blast database -nt using the blastdbcmd command. Needless to say this will take days on my rinky-dink desktop ( In an earlier I...
View ArticleBlastx With Xml Format
Hi all, I'm currently using standard alone blast, the version is ncbi-blast-2.2.25+. I tried to made xml format blast result for my downstream analysis, but I had some problems in generating it. The...
View ArticleRetrieving Protein Structures
I want to make structural analysis of lysosomal proteins found in mammals. To make start, I would like to retrieve as many structures as possible from the biological database (PDB). These structures...
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 ArticleHow To Get The Result Which Mismatch 1 To The Query Sequence By...
the program is blastn -task blastn-short -query rfam_trimed_short_uniq.fa -db /root/bio-analysis-soft/database/gss-est-db/tage -ungapped -penalty -1 -reward 1 -outfmt 6 -out 2 -num_threads 12I get an...
View ArticleAlternative to blast, faster but less sensitive?
I am looking for an alternative to blast that can search the UniProt sequence database in a faster way by losing some sensitivity. I am interesting in finding only relatively close homolog sequences,...
View ArticleHow Can I Save A Blast Record (.Xml) Into A Suitable Format For Excel (.Xls)?
I have made a BLAST search through the NCBIWWW.qblast command in Biopython. After having my results saved in a .xml format (by result_handle way, following Biopython tutorial chapter 7) I have parsed...
View ArticleCan I Have Blast Return One Hit Per Species
Hello all, I've been long troubled with redundant blast hits from different strains of the same species, for example, E. coli. These hits (can be dozens to hundreds) mask hits from other species which...
View ArticleExtracting Fasta Alignments From Parsed Blastxml File
Hello, I have cobbled together a small script that parses a BLASTxml file. It seems to parse the xml file just fine (judging from what it prints to the screen). The problem is the hsp.fas alignment...
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