Search Results for "regular expression tool"

...However, difficulties arise due to the high sequence similarity between related organisms. Further, the state of conservation of proteins between species can be correlated with their expression level which can lead to significant bias in results and interpretation. These challenges are similar but not identical to the challenges arising in the analysis of metagenomic samples and require specific solutions. pipasic (peptide intensity-weighted proteome abundance similarity correction) is a tool which corrects identification and spectral counting based quantification results using peptide similarity estimation and expression level weighting within a non-negative lasso framework. pipasic has distinct advantages over approaches only regarding unique peptides or aggregating results to the lowest common ancestor.

BIRAP (Bacterial Intergenic Region Analysis Pipeline) is an open source, easy to use Perl pipeline that can be used to re-annotate bacterial genomes using experimental data. The tool integrates expression profile derived from RNA-seq and/or proteogenomics, compares it with existing in silico annotation and helps validate annotation, identify novel protein coding regions, putative non-coding RNA as well as help correct er-rors in the existing annotation. The pipeline requires “pileup” output from SAMtools for RNA-seq data and peptide/ePST locus file (GFF) from the Proteogenomic Mapping tool for prote-ogenomics data along with the genome and existing in silico annotation. ...

...MspJI-seq_pipeline1.0 is designed to be a general-purpose mapping program to handle these special characteristics of MspJI-seq. Its alignment is based on the open source program SOAP (Short Oligo Alignment Program), and mCNNR sites recognition is performed by regular expression in perl.

ezBioNet is a biological modeling and simulation tool of molecular interaction that occurred in a cell. We aim that this software can be used for collecting biological data and making biological models to simulate it by biological researchers. ezBioNet can build a detailed biological model including signal transduction, enzyme kinetics, expression network, etc. It also support number of numerical analysis method to simulate the biological reaction networks.

Genome Expression Pathway Analysis Tool - Analysis and Visualization of Microarray Gene Expression Data under Genomic, Proteomic and Metabolic Context

dna2abc turns DNA sequences into musical sequences. The key feature is the rule editor; a rule is a regular expression paired with a Tcl script. dna2abc scans a DNA sequence, testing each regular expression: if it matches, the Tcl script is run.

Cellogica is a cellular logic analysis tool. It incorporates sequential logic and finite state machine to elucidate the relationship between transcription factors and corresponding gene expression.

Cluster Search, a program for genome-wide regular expression pattern matching.

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.

Maple Tree is a Java based visualization tool used by researchers in the biological sciences to visualize and graphically browse the results of analyses of gene expression data collected from microarray experiments.

EPTable is a simple web-based tool to analyze microarray gene expression profiles with additional gene profiles.

BIRBU (BIological Relationship BUilder) is a Java tool for microarray gene expression data analysis. BIRBU identifies biologically significant relationship between genes using microarray data and prior knowledge on relationships between genes.