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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...

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pairwise 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?

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Problem 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...

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How 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...

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How 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...

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Help 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...

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How 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....

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No 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...

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Protein 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...

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Database 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...

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blastp 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...

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human 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...

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How 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...

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How 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...

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Blast "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...

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protein 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)?

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Trinity/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...

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blast 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...

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Biopython: 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,...

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Is 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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