BLAST FATAL ERROR -database not found
I am using blastall 2.2.26 on ubuntu for local databse blast forQuery: c4_n2_train.fasta;Database: c4_n2_test.fasta;With my database files in the same directory, but still I am getting FATAL ERROR$ ls...
View Articlepairwise gene sequence similarity of all human genes
As stated, I want to get a matrix which contains pairwise gene-gene sequence similarity of the human genome genes. Are there any databases which contain this table?
View ArticleProblem with interpretation BLAST results
Hi, I'm struggling with BLAST. I'm not sure if I can properly interpret the results of BLAST. Can anyone tell me when I can be sure that the sequences of the proteins are enough similar to be...
View ArticleHow to run genome wide local blast
Hi Everyone, I have been given a task to compare one gene sequence among 50 strain of E.coli. For this study i have 50 genome scaffold file and one gene sequence file. Now my work will be compare the...
View ArticleHow to extract max score Blast hit among a huge data set?
Hi everyone, I want to extract max score blast sequence among 50 genomic data set : my approach like this:I did all the denovo assembly of all 50 genome.Next i predicted all the ORF using Prodigal: (A...
View ArticleHelp in configuring a local BLAST server.
Hi all.I am attempting to configure a local BLAST server on a Windows XP machine. I found the following series of explanations helpful but incomplete:http://www.ncbi.nlm.nih.gov/books/NBK52637/Relevant...
View ArticleHow to extract max score Blast hit among a data set?
Hi everyone, I performed a local blastp with a query protein vs 5 genome (ORF data ). Now i want to extract all the top 5 sequence automatically and make a final top hit file through awk/perl/shell....
View ArticleNo alignment in the output of blastn
Hello everybody, I am trying to BLAST a nucleotide query against a nucleotide database via command line.The problem is that, when I try blastall -p blastn -d mydatabase -i myquery I get just:BLASTN...
View ArticleProtein sequence alignment using Blast
Hi All,I am trying to run Blast over protein sequences from two organisms. I downloaded the fasta from NCBI. I am trying to iterate over the list of sequences in the fasta file and do a sequence...
View ArticleDatabase error when running blastn
Hello, as initially stated here, I am experiencing problems when I try to run the blastn command blastn -query myquery -db mydatabase.fasta.nhr.What I get is:BLAST Database error: No alias or index...
View Articleblastp with just top result from each organism
(My first Q on biostar, forgive any transgressions please!)I would like to blast a protein/aa sequence and filter(?) my results to include only the top result from each organism. I'm keen to use R or...
View Articlehuman GenBank IDs
I am working on a sequencing run that contains contamination. I did a de novo assembly and blasted the results against NR and filtered for the best hits. I now have a list of Genbank Ids. I simply want...
View ArticleHow to remove all sequences in my custom blast database?
Is it possible to clear a blast database once you have made it? I mean I created my custom database with nucleotide sequences, but I think I messed up something so I need to empty/clear my database and...
View ArticleHow to correctly speed up blast using num_threads
Hello, I did a short blast comparison using multiple cores to see how they behave. I published it in my blog and thought it would be a good idea to share it...
View ArticleBlast "Max matches in a query range" option
Hi Everyone, This is the first time I'm going to try such a web site to see if it works or not, hope it works!So I have a few questions regarding blast, I appreciate it if you can help me,I see that...
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 ArticleTrinity/RSEM/edgeR pipeline...now what?
HI people,I am a bit new to all of the Bioinformatics but so far I have produced data from the mentioned Trinity/RSEM/edgeR pipeline...I basically have 3 sample condtions -with 3 replicates...
View Articleblast for LncRNA sequence
Hi,I have some transcripts assembled by tophat and cufflink and try to find the known LncRNA from NONCODE database.I try to use blast, is them to long for blast?The other problem is that blast,blat and...
View ArticleBiopython: executing BLAST on custom DB
Ok, so I am using the NcbiblastxCommandline wrapper to execute a BLAST search on a custom database. cline = NcbiblastxCommandline(cmd='blastx', query=temp_path, out=blast_path, subject=path, outfmt=5,...
View ArticleIs there such a way/ program to do this...
Hi guys,I followed the Trinity/ RSEM/ EdgeR pipeline and have produced some FPKM spreadsheets for genes and isoforms.I am currently analysing the isoforms:I have 3 sample conditions and I am comparing...
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