Search Results for "parse-stdf"
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Showing 14 open source projects for "parse-stdf"
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Gemi
PCR primers / probes design from multiple & degenerate sequences
...Gemi accepts multiple aligned and long DNA and RNA sequences with degenerate nucleotide (non-A/C/G/T bases). Gemi can be used for quantitative, real-time and conventional PCR (qPCR, rt-PCR, etc.), and Sanger sequencing. Gemi can parse large dataset of sequences efficiently. Python codes can be supported upon request. Article: Gemi: PCR primers prediction from multiple alignments Comparative and functional genomics 2012;2012:783138 DOI: https://doi.org/10.1155/2012/783138 PMID: https://www.ncbi.nlm.nih.gov/pubmed/23316117 PMCID: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3535827/ -
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Visualization of Protein-Ligand Graphs
Compute protein graphs. Moved to https://github.com/MolBIFFM/PTGLtools
NOTE: Project moved to https://github.com/MolBIFFM/PTGLtools. The Visualization of Protein-Ligand Graphs (VPLG) software package computes and visualizes protein graphs. It works on the super-secondary structure level and uses the atom coordinates from PDB files and the SSE assignments of the DSSP algorithm. VPLG is command line software. If you do not like typing commands, try our PTGL web server: http://ptgl.uni-frankfurt.de/ -
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A set of tools for working with VCF files, such as those generated by the 1000 Genomes Project. This project is migrating to github: https://vcftools.github.io/
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qPMerge
phospho-peptide merge tools for Galaxy
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is-sfe
Information System "Supercritical Fluid Extraction"
...The final target is to help to scientists who worked with supercritical fluids to predict some useful properties such as density, solubility etc. In order to calculate molecular descriptors, parse SMILES and another applied purposes is used Chemistry Development Kit (https://sourceforge.net/projects/cdk). -
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MID Adjust
Prepare reads with no MIDs or variable length MIDs for analysis
...When you have no MIDs, or variable-length MIDs, MID Adjust appends new MIDs or extends existing ones to satisfy Pyrotagger requirements. New features include the ability to generate fake quality scores and to parse and generate QIIME mapping files. -
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DeltaQt
Parser for DELTA files (Qt, C++)
DeltaQt is part of the FreeDelta project and aims to implement a parser for DELTA (DEscription Language for TAxonomy) files using the Qt core framework. DeltaQt is a library intended to be incorporated into other applications that require the ability to parse DELTA files. -
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The goal of Ethovision Missing Samples (EMS) is to parse exported tracks from Ethovision and to report the number of missed samples in one track.
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Wattos is a collection of mostly Java programs for Structural Biology and NMR Spectroscopy. It's programs analyze, annotate, parse, archive, and disseminate experimental NMR data deposited by authors world wide into the PDB and BMRB.
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Perl Entrez Gene Parser project provides Perl parsers for NCBI's Entrez Gene based on regular expression, Parse::RecDescent, Parse::Yapp and Perl-byacc. Some can parse human genome annotations in minutes. Documentation and user guides are provided.
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A Java program to parse chemical names using IUPAC nomenclature. The output can be either a visualisation of the molecule, or in a form for other programs to use (e.g. CML).
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A Perl module that provides methods for retrieving each and every field from a standard SwissProt file.
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Swallow
A Nondeterministic GLR Parser for CUDA
...In non-deterministic parsing, more than one syntactic interpretation is valid. This is where this project comes in. The many different possible interpretations, called parses, each of which produces a parse tree, are computed in parallel using the CUDA environment. Report on Stage 1 PDF http://tiny.cc/yp5qs HTML https://docs.google.com/document/pub?id=1iHpUBOPMwvJrWQHLHhUPHmU2t5KVieq25KItU-UbMpM&pli=1 -
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danaides
Meta data extractor based on ontologies
Danaides stores meta-data from biological banks in a graph databases as well as OBO formatted ontologies. It also provides a web query interface to parse ontologies or extract nodes based on ontology requirements. Example: Get all known elements that are in family of Fish (species ontology) AND a RNA (sequence ontology).
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