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GNAT is a library and web service capable of performing gene entity NER and normalization of biomedical articles. Mentions of genes and proteins in the articles are linked to to Entrez Gene identifiers. GNAT is available both for local download (suitable for large-scale processing) and as a web ... [More]
GenomeView is a genome browser and annotation editor that displays reference sequence, annotation, multiple alignments, short read alignments and graphs. Most major data formats are supported. Local and internet files can be loaded.
This is a software that helps you to search the Ncbi Website(Enterz Databases) for your specific query making the fuss a lot simpler. All you have to do is select the type of search you want to do like on proteins or nucleotide or 3D domains or 3d structures or gene or dna or structure or gnome,etc ... [More]
GoalThe goal of this project is to summarize the function of each gene using four keywords. The source of information to find which words will be used is mainly 'geneRif' (ftp://ftp.ncbi.nih.gov/gene/GeneRIF/generifs_basic.gz). Since this file records almost 500,000 descriptions, some ... [More]
Furnace is a grid-enabled version of NCBI BLAST. Furnace takes files in FASTA format, splits them into sequences of configurable length, and submits them to a grid for processing. Each grid node runs the sequence against an instance of NCBI BLAST.
jjv is an open source gene finding application designed to annotate prokaryote genomes. It uses a two phase search; the first is a "content-based" search designed to find candidate genes and the second is a "similarity-based" search, using a known genome to compare the candidate ... [More]
GeneNetWeaver (GNW) is an open-source tool for in silico benchmark generation and performance profiling of network inference methods. GNW was used to generate the community-wide DREAM3, DREAM4 and DREAM5 In Silico Challenges.
UniPrimeOverviewUniPrime is an open-source software which automatically designs large sets of universal primers by simply inputting a GeneID reference. UniPrime automatically retrieves and aligns orthologous sequences from GenBank, identifies regions of conservation within the alignment and ... [More]
Conduct a similarity search of an input protein sequence against a nucleotide sequence database (using TblastN). This program takes a user-inputed sequence, e-value parameters, and name of a specific species database to search. The output is a list of subject ids from the matching DNA sequences ... [More]