SeqAlign.js

A Sequence Alignment Tool

Setup

OSX

Clone this repository.
Install Node.js using Homebrew.
```
$ brew install node
```
Alternatively, you can get the package direct from Node.js.
Once that's installed, install the project dependencies. In the project root directory run:
```
$ node install
```
You should now have all the dependencies installed, you're ready to go. From the project root directory, you can get more information using the following command:
```
$ ./SeqAlign.js --help
```

Linux

Clone this repository.
Install Node.js.
Go to step 3 of the OSX setup above.

Windows

I know you can install Node.js for Windows but I've never tried. Let me know how this goes.

Usage

Aligning Sequencess

An example use of SeqAlign could be as follows:

$ ./SeqAlign.js local input/PRTN200a input/PRTN200b -m ./src/scoringMatrices/BLOSUM62 -O -5 -C -2

Supplied to SeqAlign.js is the local command, this tells it to complete a local sequence alignment. Next are the two FASTA format files containing the 2 sequences to be aligned, input/PRTN200a input/PRTN200b. The -m /src/scoringMatrices/BLOSUM62 options indicates a scoring matrix to be used. -O -5 specifies a gap opening cost of -5 and -C -2 a gap continuing cost of -2 for alignment scoring.

Please use --help or -h for more information on other commands.

Testing

The tests are found in the spec directory. They can be run using:

$ npm test

craigsketchley/SeqAlignJS