Tutorial

How to use the MICROTAXI Web Server
The web server provides all of the options available in the stand-alone version. The instructions for using the web server are provided below.
Application Page
This page is designed to allow the users to submit their protein sequences either in the FASTA format using 'Genome' option, Or in the m8 format of BLAST output obtained after carrying out the BLASTP of the complete set of query proteins aginst the EggNOGsv4.0 database. These sequences will be analyzed by the microtaxi software and will predict the taxonomy of the genome on the basis of unique genes present in the genome.
Sample file: The sample file can be uploaded using the 'Upload Sample File' option.
Results Page Link
After successful upload of the file on the server, a link to retreive the results will appear as shown below. In case of a large sized input which might take a while to process, users can save the link and access their results later.
Results Page
The results will provide the summary of the analysis and links to download the result files as shown below.
HOW TO USE THE STANDALONE PROGRAM
How to install:
The installation instructions are provided on the Download page.
Command line usage for running MICROTAXI
./microtaxi <infile> <data_type>

infile: Input file containing either the protein sequences or the BLAST output in m8 format.

data_type: Specify 1 or 2. "1" if the input is the BLAST output of the complete genome in m8 format and "2" if the input is the protein sequences of the complete genome.

FILE FORMATS AND DESCRIPTION
Input file format 1 The protein sequences should be in fasta file format.
>r1|info1|info2
SQKLILDKLSFSVPKNSITSILAPNGSGKTTLLKCLLGLLKPLEETEIKACNKDILPLKPYEKAKLI

The ‘info’ in the above example is any information which the user wishes to specify in the annotation line. If the sequences are not in FASTA format or contain any character other than usual amino acid and nucleotide letter codes, the file will not be accepted and an error message will appear.

Input file format 2 BLAST output in m8 Format.
protein_1	abcdef	30.00	 90	57	3	414	500	613	699	0.16	41.2 
The above line presents a sample of the m8 format. The description of the different fields in the m8 format is provided below.
query name subject_name %_identity aligned_length #_mismatched_pos. #_gap_pos. query_seq._start query_seq._end subject_seq_start subject_seq_end e-value bit_score
NOTE : THE UPLOADED FILE NAME SHOULDN'T HAVE ANY BLANK SPACES (for e.g. "sample file" is not allowed)
OUTPUT FILES

Descriptions of the output files.

*.Taxa: This file contains the predicted taxonomy of the submitted query genome arranged in the order of ranks.