Bioclojure

Bioclojure provides functional Clojure libraries for manipulation and analysis of biological sequence data, supporting parsing of UniProtXML, Genbank XML, FASTA and FASTQ and integration with BLAST, SignalP, TMHMM and InterProScan outputs for bioinformatics research.

Key Features:

• Format support: Native support for UniProtXML, Genbank XML, FASTA, and FASTQ formats.
• Parsers and accessors: Parsers and accessors for seamless programmatic manipulation of sequence and annotation data.
• Tool wrappers: Wrappers for external analysis programs including BLAST, SignalP, TMHMM, and InterProScan.
• Output parsing: Parsers for the outputs produced by BLAST, SignalP, TMHMM, and InterProScan.
• Functional programming: Leverages Clojure's functional programming style with emphasis on laziness and composability.
• Concurrency: Uses concurrency mechanisms to enable processing of large datasets.
• Thread-safe pipelines: Enables creation of thread-safe, composable pipelines that chain built-in and user-defined functions with lazy evaluation.

Scientific Applications:

• Bioinformatics research: Programmatic manipulation and analysis of biological sequence datasets for research purposes.
• Sequence analysis: Parsing and downstream analysis of UniProtXML, Genbank XML, FASTA, and FASTQ sequence data.
• Functional genomics studies: Integration of sequence data with outputs from BLAST, SignalP, TMHMM, and InterProScan for functional genomics analyses.

Methodology:

Provides parsers and accessors for UniProtXML, Genbank XML, FASTA and FASTQ; wraps BLAST, SignalP, TMHMM and InterProScan and parses their outputs; implements Clojure-based functional, lazy, composable and thread-safe pipelines with concurrency.