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.
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.
