fastacmd error error cannot initialize readdb for nr database Henley Missouri

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fastacmd error error cannot initialize readdb for nr database Henley, Missouri

What'S The Different Between Formatdb (In The Legacy Blast) And Makeblastdb (In Blast+)? Any help much appreciated :-) Thanks

0 0 06/20/14--09:06: Obtaining the top matches from blast Contact us about this article Hi, I have downloaded the current version of the stand-alone-blast My genome sequence i make it as subject instead of makeblastdb and the command is like this $tblastx -query /home/hazel/Dekstop/heterobasidion.fasta -subject /home/hazel/Dekstop/Gano.fasta -out tblastx_Result.txt -outfmt 1 My own genome sequence contain Contact us about this article For example, I am running standalone Blast+ for thousands of EST sequences with remote (NCBI) server.

These smaller databases can be searched as if they were a single entity using: blastall -i infile -d hugefasta -p blastn -o out In this case, BLAST recognizes that the database I want to run over local Blast but getting some error, I would greatly appreciate some suggestions. '''from Bio.Blast.Applications import NcbiblastxCommandline help(NcbiblastxCommandline)''' from Bio.Blast.Applications import NcbiblastpCommandline from StringIO import StringIO from Please don't fill out this field. However, I am interested on only the top 3 matches.

Ncbi Legacy Blast Usage With Tblastn/Pssm I'm trying to get a webservice for protein discovery running. For this I need the Round attribute shown in> The biopython tutorial says: "In Biopython, the parsers return Record objects, either Blast or PSIBlast depending on what you are I expect to find huge, contiguous hits for some BACs in the genome. The Latest Version: Make sure you are using the latest version of the formatdb executable.

If you need to use the -o T option then your best option is to examine the definition lines of the database sequences and attempt to make them conform the FASTA My aim is to extract theses hit-contigs from the original fasta-file with all contigs. I followed the instructions at: > > > > but when I tried the tests i.e. For the new BLAST+ distribution use "blastdbcmd" $ blastdbcmd -db myBlastDBName -dbtype prot -entry_batch myContigList.txt -outfmt %f -out myHitContigs.fasta Again you could omit the '-dbtype prot' and let the program guess.

I do not have a list of these files as they are within the folders. I added a ">" to every ID, but still there is the same error. I didn't know why my sequences were'nt found in a certain database...:( Yes, I believe that is true. I think for the older blast version you use formatrpsdb and it´s create others files including .aux, but for this new version I dont know what to use.

The -outfmt %f tells the program to output sequences in FASTA format; you could also omit this since this is the default output format. See my post above about how to make your the entries in your query list unique using the sort command. Once a source database file has been formatted by formatdb it is not needed by BLAST. I have formatted a nucleotide database using makeblastdb.

You would have to use gi numbers (if they existed in the original fasta file) to retrieve sequences. In the tabular output, there is query sequence match start and end point as well as subject sequence start and end point. if there are any? Your blastx command should look like $ blastx -db myDB -query myQuery -out myContigList.txt -outfmt "6 sallacc" [other blastx options] If you had multiple sequences in your query file the resultant

I am trying to extract sequences from a file containing a list of IDs. blast • 2.4k views ADD COMMENT • link • Not following Follow via messages Follow via email Do not follow modified 4.5 years ago • written 4.5 years ago by Sakti In order to use the formatdb option -o T, especially for use with NCBI tool kit retrieval tools the FASTA defline must follow a specific format. You seem to have CSS turned off.

The program reports '1' if present, '0' if absent next to gene name in the output. For the new BLAST+ distribution use "blastdbcmd" $ blastdbcmd -db myBlastDBName -dbtype prot -entry_batch myContigList.txt -outfmt %f -out myHitContigs.fasta Again you could omit the '-dbtype prot' and let the program guess. Finally - there are easier ways to extract sub-sequences from larger sequences (using the original FASTA file) than dumping from a BLAST database. F.

To eliminate the redundancies in this list you can use the sort command with the unique filter. $ sort -u myContigList.txt > myContigList_uniq.txt You could now use the myContigList_uniq.txt file in To get the text-file with the ID I used the command -outfmt "10 qgi". Volklor02-08-2012, 05:28 PMYour response to Anna is almost helpful to me...I have been using perl to extract seqs, but a one-liner, if it works, will be so much more efficient! Contact us about this article Very simply, what are the units of the alignment length reported by BLASTX and BLASTP?

Hazel_Tan11-06-2014, 05:16 AMAnna, You can do this yourself and it would be a good learning exercise, but since you have already made a BLAST database of the contigs, NCBI has kindly Extension      Content           Format            --------------------------------------------- Nucleotide database formatted without "-o T"                                     nhr         deflines    binary                                                                                nin           ISAM        binary  Terms Privacy Opt Out Choices Advertise Get latest updates about Open Source Projects, Conferences and News. I am having an extremely difficult time with formatdb and fastcmd from NCBI blast.

Content Search Users Tags Badges Help About FAQ Access RSS Stats API Use of this site constitutes acceptance of our User Agreement and Privacy Policy. Simple test: open a shell: ls $BLASTDB should give something like:: formatdb.log nr.00.pnd nr.00.psq nr.01.pni nr.pal pdbaa.pnd pdbaa.psq swissprot.pnd swissprot.psq ... You seem to have CSS turned off. B.) Note on "SORTFiles failed" message: Formatdb will use the 'standard' temporary directory to sort the string indices on disk.

H. Here's the command I use - blastn 80BACs.fasta -db mygenome -out 80BACsBLAST -outfmt 10 -num_threads 8 -evalue 10e-3 -index_name mygenomeMBI Around 10 minutes after it starts running, the program halts after I'm running this on a Mac server with 2 Quad-core Intel processors with 16GB RAM. 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 equivalent of -F

The "-b" option, if TRUE, specifies that       input ASN.1 database is in binary format. Help with custom database of a genera and count of hits (NGS, 454) Hello biologists and bioinformaticians around the world! David

0 0 05/10/13--12:32: Are Alignment Lengths Reported In Ncbi Blast+ Results Counting Nucleotides Or Amino Acids? computer is a macpro with 2 quad-core intel xenon processors, 16 GB of RAM.

If this is the case for you, do not be surprised when fastacmd generates an empty output file. Anna, You don't want to use outfmt 10 (comma separated values), you want outfmt 6 (tabular data w/o headers). These ancillary commands should have been installed when you installed BLAST Old school use the command "fastacmd" $ fastacmd -d myBlastDBName -p protein -i myContigList.txt -o myHitContigs.fasta You can omit the Contact us about this article I started to run blast, locally on my machine, on 4 files with 1323, 210, 501, 166 fasta sequences each.

Examples of illegal ID's would be: H.sapiens|seq1 gnl|H.sapiens|seq1|A The first identifier is missing a database tag (e.g., no "lcl"), the second identifier has an extra field since vertical bars separate fields.  The procedure to produce an alias file for searching (protein) nr limiting it to a list of zebrafish GI's would be: 1.) obtain the list of zebrafish GI's from Entrez or aliealexandre02-20-2011, 08:22 PMGreat !! I used formatdb, so does the same issue apply there?

I would like to perform a tblastn w...