#NCBI-taxcollector

Collects and Attaches NCBI taxonomy information to BLAST and SOAP2 results.

Results must be in tabular format (-m 8 or -m 6)

By: Raquel Dias and Marcelo V. Neves

Contact: [email protected]

Pontifical Catholic University of Rio Grande do Sul - Brazil

High Performance Laboratory (LAD PUCRS)

#DESCRIPTION

A Tool for parsing sequence search results and collecting information on NCBI taxonomic data

Project home page: https://github.com/Bioinfo-Tools/NCBI-taxcollector

Operating system(s):Platform independent

Programming language: Perl and C

License: GNU GPL

#REQUIREMENTS

• Perl 5 or higher
• C compiler

#INSTALL

• Download NCBI-taxcollector main functions

$ wget https://github.com/Bioinfo-Tools/ncbitc_functions/tarball/master

• Extract

$ tar -xvf master

• Go inside the extracted folder

$ rm master

$ mv Bioinfo-Tools-ncbitc_* master

$ cd master

• Compile

$ make all

• Copy the binary named "tax_class" to the same dir as taxcollector_ncbi-0.01.pl

$ cp tax_class ../

$ cd ..

• Change the exec permissions

$ chmod 777 tax_class

• Download NCBI taxonomy databases

$ wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz

$ wget ftp://ftp.ncbi.nih.gov/pub/taxonomy//gi_taxid_nucl.dmp.gz

• Extract the databases

$ tar -xvf taxdump.tar.gz

$ gunzip gi_taxid_nucl.dmp.gz

Convert dump files to binary

$ ./tax_class -c

• Usage

$ perl taxcollector_ncbi-0.01.pl -f Classification results (tabular text file) -o Output file

#EXAMPLES

• Input example:

        S001416244	gi|309261160|gb|HQ246245.1|	81.87	1186	148	64	226	1375	128	1282	0.0	 937
        S001416244	gi|85001901|gb|DQ337083.1|	78.63	1535	218	99	1474	1	1486	0.0	 917
        S001416244	gi|309261186|gb|HQ246271.1|	81.00	1216	137	75	247	1400	213	1396	0.0	 880
  

• Output example:

        S001416244	[0]Bacteria;[1]Proteobacteria;[2]Alphaproteobacteria;[3]Rhodospirillales;[4]Acetobacteraceae;[5]Roseomonas;[6]Roseomonas_sp._6A18S6;		81.87	1186	148	64	226	1375	128	1282	0.0	 937
        S001416244	[0]Bacteria;[5]uncultured_bacterium;[6]uncultured_bacterium;	78.63	1535	218	99	1	1474	1	1486	0.0	 917
        S001416244	[0]Bacteria;[1]Firmicutes;[2]Bacilli;[3]Bacillales;[5]Exiguobacterium;[6]Exiguobacterium_sp._8A18S8;		81.00	1216	137	75	247	1400	213	1396	0.0	 880