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System: ALAE

Introduction
ALAE is an efficient software that can guarantee to find all local alignments of biosequences. It was implemented using GNU C++.

Features

The released source supports the following features: 
       - build BWT index for text       
       - build domination relations for text
       - save indexes and domination relations in disk and load indexed from disk 
          to memory
       - local alignment between biosequences

Download

The source code of ALAE is available here for download. The software has been tested on a Linux environment (Ubuntu).

For 32 bits Linux: ALAE-x32-linux.tar.gz
For 64 bits Linux: ALAE-x64-linux.tar.gz

To compile the software:

make

The following binaries will be generated:

    bwt_build                 Build BWT index and save the index to disk
    dominate_build         Build domination relations and save them to disk 
    alae                         Perform local alignment search
 
We also provide example data here: example data
The example data includes a 10M file text10M.txt as a text sequence and a 10K file query10K.txt as a query sequence.

Requirements
The code could be run in Linux (32 bits/64 bits) using g++ complier.

Step-by-Step Instruction

Run "./make" to compile the code and generate the three executable files.

Build BWT Index

Run command "./bwt_build <text file> <output index file>" to generate two index files
         - indexName for storing BWT sequence 
         - indexName.sa for storing SA arrary

For example, run "./bwt_build text10M.txt text10M.index" to build BWT index for our example data. text10M.index and text10M.index.sa will be generated.

Build Domination Relations

Run command "./dominate_build <bwt index file>" to generate a index file
         - indexName.dominate for storing domination relations

For example, run "./dominate_build text10M.index" to build domination relations for our example data. text10M.index.dominate will be generated.

Perform Local Alignment Search

ALAE parameters are listed by typing “./alae”.

Syntax: alae <index file> <query file> <output file>
               -H <cutoff score>
               -R <reward for a match>
               -Q <penalty for a mismatch>
               -G <cost to open a gap>
               -E <cost to extend a gap>

The default setting of ALAE are 18 for cutoff score, <1,-3,-5,-2> for the scoring schema. For example, run "./alae text10M.index query10K.txt result.txt" to perform local alignment for our example data.

Datasets
We used three datasets in our experiments, which are
human genomes, mouse genomes and protein database UniParc.


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