Search Results for "genes"

This package includes a few programs for rapid functional annotation for metagenomic sequences, including, 1) Gene prediction by FragGeneScan; 2) Similarity search by RAPSearch2; 3) Functional annotation in GO (Gene Ontology) and EC (Enzyme Commission) based on similarity search results; 4) From EC to metabolic pathway reconstruction by MinPath. Inputs: Just sequencing reads (or assemblies) Outputs: Protein-coding genes (or gene fragments); similarity search; functional annotations (in GO...

* GSA-SNP2 is a successor of GSA-SNP (Nam et al. 2010, NAR web server issue). GSA-SNP2 accepts human GWAS summary data (rs numbers, p-values) or gene-wise p-values and outputs pathway genesets ‘enriched’ with genes associated with the given phenotype. It also provides both local and global protein interaction networks in the associated pathways. * Article: SYoon, HCTNguyen, YJYoo, JKim, BBaik, SKim, JKim, SKim, DNam, "Efficient pathway enrichment and network analysis of GWAS summary data using...

ParBiBit is a parallel tool to accelerate the search of biclusters on binary datasets, especially useful for gene expression data. This tool receives as input the expression values of n genes and m samples in a file with ARFF extension and returns a file with the biclustering information.

MPICorMat is a parallel tool to construct correlation similarity matrices as part of the procedure to generate gene co-expression networks. This tool takes as input a matrix with the expression values (a float value) for different genes observed from several samples. It is a parallelization of the first module of the RMTGenNet tool (https://github.com/spficklin/RMTGeneNet). RMTGeneNet users can exchange this CCM module by MPICorMat, benefit from its fast computation to generate the similarity...

This software is intended to identify the differentially expressed genes from the given set of genes. The data is input by the user in the form of Comma Delimited (.csv) Microsoft Excel (2007 and above) File.

MPIGeneNet is a parallel tool to construct gene co-expression networks using Pearson’s correlation and Random Matrix Theory (RMT). This tool takes as input a matrix with the expression values (a float value) for different genes observed from several samples. It is a parallelization of RMTGenNet tool (https://github.com/spficklin/RMTGeneNet). MPIGeneNet integrates the whole procedure of creating the in one program, which makes the tool easier to work with (the users only have to launch...

This is a Naive Bayes text classifier library to C++, you can classify SPAM messages, genes, sentiment types in texts. Naive Bayes has been studied extensively since the 1950s. It was introduced under a different name into the text retrieval community in the early 1960s, and remains a popular (baseline) method for text categorization, the problem of judging documents as belonging to one category or the other (such as spam or legitimate, sports or politics, etc.) with word frequencies...

HPeak is a hidden Markov model-based approach that can accurately pinpoint regions to where significantly more sequence reads map. Testing on real data shows that these regions are indeed highly enriched by the right protein binding sites. Command (single-end): perl /compbio/software/HPeak3/HPeak.pl -sp HUMAN/MOUSE -format BED -t TREATMENT.inp -c CONTROL.inp -n OUTPUTPREFIX -fmin 100 -fmax 300 -r 36 -ann -wig -seq -interfiles Command (pair-end): perl /compbio/software/HPeak3/HPeak.pl -sp...

Turn genes into rhythm. Feed the software with a nucleotide sequence as input, and it will translate it as MIDI messages, designed especially for the KORG ESX-1 but ready to be used with any MIDI-enabled device or software.

PeakAnnotator was designed for bulk annotation of genomic locations, to identify key features of interest, such as location within genes or closest up- or downstream transcription start site.

FastEST - A software tool for clustering Expressed Sequence Tags (EST). The motivation is to identify genes from DNA-fragments.

A personal genealogy application for use on (primarily) Linux systems. Data is read from a GEDCOM file and shown in a GUI. This project is still in alpha, so any help is welcome.

Zeeble Bug is a basic A-life program designed for lava-lamp style desktop viewing of a pond filled with "bugs". It employs a simple neural networks, genes, and varied water conditions to keep the pond a shifting and evolving entity.

DEODAS designs & analyzes consensus-degenerate oligonucleotide probes for biological research. DEODAS automatically designs and screens, probes against databases of known genes & stores the information in a searchable database.

A biological data warehouse that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. Website: http://bioinformatics.ubc.ca/atlas