Search Results for "cli-parser"

...This tool allows bioinformatics researchers to efficiently distribute their mapping tasks over the nodes of a cluster by combining a fast multithreaded spliced aligner (HISAT2) with Apache Hadoop, which is a distributed computing framework for scalable Big Data processing. HSRA currently supports single-end and paired-end read alignments from FASTQ/FASTA datasets. Moreover, our tool uses the Hadoop Sequence Parser (HSP) library (link above) to efficiently read the input datasets stored on the Hadoop Distributed File System (HDFS), being able to process datasets compressed with Gzip and BZip2 codecs.

KAnalyze is a Java toolkit designed to convert DNA and RNA sequences into k-mers. It is both a command line application and an API.

A protein contact matrix is 2D representation of the distances between amino acid residues in a 3D protein structure. Protein Contact Map Generator (PCMGen) is a command line tool which takes protein 3D structures (PDB format files) as input and computes contact distances between two chains (from single or two different proteins). These matrix files can be further visualised as Contact Maps using other visualization tools/ programs (like R-heatmaps). Contact Maps can be used to understand...

We present an alternative library for development of bioinformatics Java applications. a Java implementation of JGBParser was built. It consists in a library, able to analyze text files in the GenBank Flatfile (GBF) format.

The code here is a parser for CALBC corpus into Java object.

This project develops a web-based (JSP) Fuzzy Rule-Based Expert System for analyzing ECG (electro cardio gram) signals & diagnosing Tachi-Arrhythmias. Proj. main blocks: inference engine, knowledgebase, KB editor, explanation, and feature extraction.

OpenDMAP (Open Source Direct Memory Access Parser) is a natural language processing (text mining) application: a semantic parser for information extraction.

A bioinformatics package to analyse ESTs (Expressed Sequence Tags) easily. It contains functionalities of ESTs for EST submission, Batch BLAST and BLAST result parser, etc. easiEST contains JAVA GUI applications for analysing ESTs or other sequences