Dr. Chaochun Wei, Department of Bioinformatics and Biostatistics


I. What is ALTSCAN?
Alternative Splicing SCANner (ALTSCAN) is an ab initial alternative splicing predictor whose primary purpose is to explore protein-coding structures as many as possible. It is an extended GHMM.
ALTSCAN have a great capability of detecting novel transcripts with coding potentials when integrated with RNA-seq data.
ALTSCAN predictions can be found here.

II. Installation
ALTSCAN has been tested on Linux OS. Please install it as follows.
Step 1 Download ALTSCAN package from here.
Step 2 Decompress the package as
tar -zxvf altscan_v1.0.tar.gz
Then you'll get a directory named altscan_v1.0/
Step 3 Compile
cd altscan_v1.0/
Then you can find an executable altscan in directory bin/

An example has been provided to show how to run ALTSCAN. You can find an example file named example.fa under the example/ directory.It will be used as the input of ALTSCAN.
You have two ways to use ALTSCAN. We recommand the second method.

(1) run ALTSCAN directly.
cd bin/
./altscan ../parameters/human.zhmm ../example/example.fa -top >../example/example.altscan
The raw ALTSCAN result is included in example/.
A filter step is needed to remove the duplicated transcripts (two or more transcripts differ only in their UTR regions). The perl script to remove the redundant transcripts is provided in the package. The exampel command line is as follows.
perl del_rep.pl ../example/example.altscan >../example/example.altscan.filtered
The filtered ALTSCAN results are also provided in example/.

(2) Use a perl script,ALTSCAN.pl. It contains scripts to run ALSCAN and del_rep.pl automatically, and users can get the filtered result directly.
cd bin/
./runALTSCAN.pl ../parameters/human.zhmm ../example/example.fa >../example/example.altscan.filtered

IV. ALSCAN options
ALTSCAN's default settings for the TOP number is 100, you can use change_top_N.pl in bin/ directory to set the TOP number as you wish. For example, we want to set TOP number to 250:
cd bin/
./change_top_N.pl 250
cd ..
make clean
Now the TOP number is set to 250.

Citation. Please cite this paper if you use ALTSCAN predictions. ==================================================
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©2010 Chaochun Wei