Search Results for "regular expression tool"

We developed a novel clustering-free method, microarray-associated motif analyzer (MAMA), to predict novel cis-acting elements based on weighted sequence similarities and gene expression profiles in microarray analyses. Simulation of gene expression was performed using a support vector machine and based on the presence of predicted motifs and motif pairs. The accuracy of simulated gene expression was used to evaluate the quality of prediction and to optimize the parameters used in this...

miRNA is a widely known small non-coding RNA which can mediate gene regulation of most important biological processes in plants and animals. Therefore, identification conserve and novel miRNA and their target genes in model and new sequenced species are inevitable. MITP is designed to identify miRNA easily and faster based on sequence mapping result from any mapping software which producing SAM format output result, blast result (default output result) or blat result (default output result)....

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. ...

The microRNA Temporal Analyzer (mirnaTA) is a bioinformatics tool which can be used to identify differentially expressed miRNAs in temporal studies. It is implemented in Perl and R package (>= 2.13.0) and can be run across multiple platforms such as Linux, Mac and Windows. The mirnaTA requires that users provide data from a minimum of two time points and analyze up to 20 time points. To normalize data and remove technical variability, Normal Quantile Transformation (NQT) was used, and the...

This project contains a set of php/perl scripts to analyze Cisco IOS-XR routers PE configuration, providing an html output which is very useful to surf over configurations. Moreover, it contains some other functions to search and compare configurations (access-list, prefix-sets, route-maps ...) between XR and IOS routers, and to analyze syslog data. It is not intended for "normal" end-users, but for network administrators and operations groups. You will need to install Apache (or any...

...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.

Geographic tag manipulator - a simple XSLT-based tool to add, remove, or change tags of OpenStreetMap objects.

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

The Perl Formal Language Toolkit (FLaT), is a set of compatible Perl modules used for investigating regular expressions and finite automata. It is also a goal to create a tool kit, which may be used to create apps with FAs as underlying data structures..

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.