AITrans

Assessing Insect Transcriptomes



1. INTRODUCTION


AITrans is a pipeline for assessing the quality of insect transcriptomes which generated by sequencing technology and it is running on Linux platform.

There are 4 modules as below:
- AITrans.pl
- blast_parsing.pl
- categorized_LR50_C50.pl
- run_inparanoid.sh

2. INSTALL


2.1 Third-party software packages for AITrans.

- perl (version 5.10 or later versions)
- bioperl (version 1.006901 or later versions )
- NCBI-BLAST+ (version 2.2.25+ or later versions)
- netstart (version 1.0c or later versions)
- inparanoid (version 4.1 or later versions)

Please follow the instructions to install the packages.

2.2 Unpack AITrans.tar.gz

$ tar -xzvf AITrans.tar.gz

2.3 set environment variable

  • Set shell environment variable:
    export INPARANOID=path/to/inparanoid_4.1
    export AITrans=path/to/AITrans

  • And add $AITrans/bin to system variable:
    PATH=$AITrans/bin:$PATH

  • Add BLAST+ bin directory to system variable:
    PATH=/path/to/BLAST+/bin:$PATH

  • After the netstart was installed, add bin directory to system variable:
    PATH=/path/to/netstart/bin:$PATH

3. RUNNING AITrans


$ AITrans.pl -t < Transcriptomes.nucleotide.fa > -g < GenomeReferenceSpecie.protein.fa > \
                   -d < Database for transcriptome annotation >

Transcriptomes.nucleotide.fa: fasta formate.
     Transcriptome nucleotide sequences which you want to assess.

GenomeReferenceSpecise.protein.fa: fasta formate.
     Genome reference specie is the specie whose genome had been sequenced and well annotated.
     And this specie was closed to the specie whose transcriptome you want to assess.

Database for transcriptome annotation: protein database.
     NR database or other database which was used to annotate the transcriptome.

When program finished, the results was input into two files, which will be created in the directory “aitran_out”:
     - summary.xls
     - Translation_pep.fasta

NOTE: Two step in this pipeline are very slowly. One is the annotation step, another is inparanoid running time.      You can set more cpu number to accelerate the first step. And for the second step, you can change this line      in the inparanoid.pl file:
          $blastall = "blastall"; #Add -aN to use N processors
     to
          $blastall = "blastall -a4"; #Add -aN to use N processors
     to add the blast processors number.

4. DOWNLOAD



Please contact me if you are interested or hava any problem in AITrans.