Projects

GNAT NER

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] service (suitable for more limited processing or testing). A combination of local and remote processing is also available, where CPU-heavy operations are performed locally and memory-intensive operations are performed remotely (this is suitable for large-scale processing where a large amount of memory is not available). GNAT uses LINNAEUS (Gerner et al., 2010) for species detection and BANNER (Leaman et al., 2008) in one part of its false positive filtering process. [Less]

GenomeView

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.

ncbi

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] and type in the name or the keyword you want to get the information for and it fetches the result for you. Genome specific researches can be carried out.Est databases can now be accessed without any hassle. It is faster over the conventional web browser method. Two or more results ca be compared at the same time with the help of a Desktop Pane The Software is available under the GNU GPL V3 [Less]

genequad

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] different approaches will need to be tested. This project has been divided into two subprojects GenDex and GeneQuad. Project DescriptionMain activities can be seen in the ActivityLog. Project in ActionWatch the Rails web application made to interface with the data acquired through GeneQuad (http://rails-dev.bioinformatics.northwestern.edu/app-name/genequad) and GenDex (http://rails-dev.bioinformatics.northwestern.edu/app-name/gendex) [Less]

furnace

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

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] genes with and to judge the probability that they are indeed genes. [Less]

GeneNetWeaver

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.

uniprime

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] generates suitable primers that can amplify variable genomic regions. UniPrime differs from previous automatic primer design programs in that all steps of primer design are automated, saved and are phylogenetically limited. We have experimentally verified the efficiency and success of this program. UniPrime is an experimentally validated, fully automated program that generates successful cross-species primers that take into account the biological aspects of the PCR. The current version is UniPrime 1.18 (Prune / April 2nd, 2008). DocumentationText files associated with the UniPrime: README INSTALL LICENSE. DownloadThe Linux/Unix code is publicly available. Before installing UniPrime, your system must be compliant with the following requirements: Perl 5.005 or later. BioPerl modules: UniPrime uses functionality provided in BioPerl modules. Primer3 is mandatory since UniPrime is based on Primer3. T-coffee is mandatory if you plan to use multi-alignment option. PostgreSQL is mandatory since UniPrime store all the sequences, alignments and primers in a database. Once you download, uncompress (bunzip2), and un-tar (tar xf), see the file INSTALL for the installation instructions. TutorialHere is a simple example of a full execution of UniPrime. Each step can be reviewed with the web-companion interface. For a complete explanation consult the file README. 1. Added a new locus and use the human OAZ1 gene as prototype. The GeneID (4946) is retrieved from GenBank (from the command line in a Terminal window): ./uniprime.pl --action=locus --target=4946 -v2. Use the locusID L3.1 (case sensitive) and look for orthologues within the class Mammalia and an e-value of 2e-50 as threshold: ./uniprime.pl --action=ortho --target=L3.1 -e=2e-50 --query=Mammalia[ORGN] -v3. Use the locusID L3.1 and establish an alignment and a consensus sequence with a threshold of 60%: ./uniprime.pl --action=align --target=L3.1 -c=60 -v4. Use the locusID L3.1 and design the primer set: ./uniprime.pl --action=primer --target=L3.1 -v5. Optionally, use the primer set X3.2 and do a virual PCR within the Class Mammalia of the WGS databank of the NCBI. ./uniprime.pl --action=vpcr --target=X3.2 --db=wgs --query=Mammalia[ORGN] -vWant More?See the BatLab and Web services. [Less]

itamming

Visualization of sequence and motif data. University of Tartu. Flash.

genefamilyfinder

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] ((over a certain e-value) and a list of the fasta sequences (accessed using the fastacmd) [Less]