Pairwise Sequence Aligner

This project consists of:

• An abstract framework to compute sequence alignments.
• An implementation of the pairwise alignment algorithms for local, global, repeated and overlap global, plugged into the framework.
• A series of front end applications which (leveraging on the framework) allow end users to align sequences.

ReactJS Application

• Web application built using Javascript, React and Material UI.
• A hosted version can be found at: https://pairwise-alignment.herokuapp.com/

Usage

• Launch the web server by issuing the following command from the cloned project directory:

./gradlew bootRun

• Alternatively you can launch the web server by issuing the following command that starts a docker container with the appropriate docker image:

docker run -p 8080:8080 marcoruiz/align-ws:master

• Point your browser to http://localhost:8080/
• Enter the parameters of the alignment and press the Align button

Web Service Application

• Spring boot based REST web service.
• The requests are submitted using POST verb (rather than GET) since the sequences to aligned may be lengthy.
• By default the web service runs on port 8080, and the resource URI is api/align.

Usage

• Launch the web service by issuing the following command from the cloned project directory:

./gradlew bootRun

• Alternatively you can launch the web server by issuing the following command that starts a docker container with the appropriate docker image:

docker run -p 8080:8080 marcoruiz/align-ws:master

• Submit a POST web request to the running web service (by default http://localhost:8080/api/align) with a payload such as the following:

{
  "sequenceA" : "TNAKTAKVCQSFAWNEENTQKAVSMYQQLINENGLDFANSDGLKEIAKAVGAASPVSVRSKLTS",
  "sequenceB" : "STVSPVFVCQSFAKNAGMYGERVGAVGAASPVSCFHLALTKQAQNKTIKPAVTSQLAKIIRSEVSNPPA",
  "scoringMatrixName" : "BLOSUM62",
  "alignmentType": "LOCAL",
  "maxNumberOfSolutions" : 50,
  "fixGapPenalty" : 12,
  "varGapPenalty" : 2,
  "minScore" : 10
}

• From the command line you could issue a curl command like the following:

curl 'http://localhost:8080/api/align' -i -X POST -H 'Content-Type: application/json' -d \
'{
  "sequenceA" : "TNAKTAKVCQSFAWNEENTQKAVSMYQQLINENGLDFANSDGLKEIAKAVGAASPVSVRSKLTS",
  "sequenceB" : "STVSPVFVCQSFAKNAGMYGERVGAVGAASPVSCFHLALTKQAQNKTIKPAVTSQLAKIIRSEVSNPPA",
  "scoringMatrixName" : "BLOSUM62",
  "alignmentType": "LOCAL",
  "maxNumberOfSolutions" : 50,
  "fixGapPenalty" : 12,
  "varGapPenalty" : 2,
  "minScore" : 10
}'

Swing Application

Usage

• Launch the swing application by issuing the following command from the cloned project directory:

./gradlew run

• The initial interface provides you with inputs to specify the parameters for the alignment to compute:

  1. Sequence A and Sequence B to be aligned. The application comes preset with a couple of example sequences in these fields (for demo purposes).
  2. Scoring matrix to be used (BLOSUM 50, BLOSUM 62 or PAM 250)
  3. Values for gap penalties.
  4. Cut solutions parameters.
  5. Type of alignment to be applied (Local, Repeated Local, Global, Overlap Global)

• Once you are ready to run the alignment just press the Run Pairwise Alignment! button. The application will switch to the results view, presenting the following information:

  1. A graphical view (Alignment Plot) of the currently selected alignment solution.
  2. A drop down control to select which one of the alignment solutions computed to currently explore.
  3. Statistics about the currently selected alignment solution (score, positives, identities, length and sequences sizes).
  4. A textual representation of the currently selected alignment solution. The format is similar to FASTA.