TP Bioinformatica - UTN FRBA

Running as a Script

You only need Java 1.8 to run the release.

• Translation from mRNA to the corresponding protein sequence:

java -jar ./releases/bio-tp-v1.0.jar \
    transcription \
    --input ./releases/SOD1_mRNA_NM_000454.gb \
    --output ./releases/result/protein_seq.fas

• Search for alignments via NCBI QBlast service:

java -jar ./releases/bio-tp-v1.0.jar \
    alignment \
    --input ./releases/result/protein_seq.fas \
    --output ./releases/result/alignments_1.txt \
    --index 1

• Search for alignments via Local DB:

java -jar ./releases/bio-tp-v1.0.jar \
    alignment local \
    --input ./releases/result/protein_seq.fas \
    --output ./releases/result/alignments_1.txt \
    --dbpath /path/to/db

** In order to search alignments with a local DB you need to have in your local blastall with blastp program installed and the swissprot DB with Blast formatted.

• Search for protein translations via EMBOSS coderest:

java -jar ./releases/bio-tp-v1.0.jar \
    emboss-translation \
    --input ./releases/SOD1_mRNA_NM_000454.gb \
    --output ./releases/result/translations_from_emboss \
    --embossdir /path/to/emboss/programs

• Search for motifs from protein translations via EMBOSS patmatmotifs:

java -jar ./releases/bio-tp-v1.0.jar \
    emboss-motifs \
    --input ./releases/result/translations_from_emboss.prot \
    --output ./releases/result/result.motifs \
    --embossdir /path/to/emboss/programs

Building the app

Development dependencies:

• JDK 1.8
• Scala 2.12.2
• SBT >= 0.13.13

You need to generate a Fat Jar with Assembly:

• Run sbt assembly from the project root.

The fully executable JAR will be in /target/scala-2.12/ ready to rock.

How to get Blast and the swissprot DB in your local

Exposed by NCBI