Bioinformatics Links Directory : Other Resources

Resources include databases, gene-collections, portals, and various tools related to the human genome.

BEARR - (Found June 19, 2008 )

Batch Extraction and Analysis of cis-Regulatory Regions (BEARR) takes a list of gene identifiers (such as RefSeq and Unigene IDs), consensus patterns, and (optionally) a position weight matrix as input and returns a list of matches for the patterns in both the sense and anti-sense strands of the relevant genomic sequence. The user specifies what distance up and downstream from both the transcription start site and the 3' terminus to look for the patterns.
http://giscompute.gis.a-star.edu.sg/~vega/BEARR1.0/

Mammalian Gene Collection - (Found June 19, 2008 )

Goal is to provide a complete set of full-length (open reading frame) sequences and cDNA clones of expressed genes for human and mouse; publicly accessible.
http://mgc.nci.nih.gov/

Medical Acronym Finder - (Found June 19, 2008 )

The acronym database provides free access to medicalbiological acronyms. It has 100,000+ acronyms and the users can also contribute by rating the entries quality. In the backend, it is generated from medline data.
http://bioinformatics.org/textknowledge/acronym.php

MHCPred - (Found June 19, 2008 )

Major Histocompatibility Complex Predictor (MHCPred) predicts the binding affinities of major histocompatibility complexes to ligands.
http://www.jenner.ac.uk/MHCPred/

PrimerStation - (Found June 19, 2008 )

PrimerStation is a multiplex genomic PCR primer design tool specific for the human genome.
http://ps.cb.k.u-tokyo.ac.jp/

SBT Interface - dbMHC - (Found June 19, 2008 )

The SBT (Sequencing-based typing) interface is a tool accompanying the NCBI's Major Histocompatibility Complex database (dbMHC). It identifies the allelic composition of sequence-based typing (SBT) results of cDNA or genomic sequences. Samples are compared with databases containing all known alleles for several human leukocyte antigen (HLA) and killer cell immunoglobulin-like receptors (KIR) loci. An interactive sequence viewer allows inspection of the alignments.
http://www.ncbi.nlm.nih.gov/mhc/sbt.cgi?cmd=main

SOURCE - (Found June 19, 2008 )

Stanford Online Universal Resource for Clones and ESTs pools publicly available data commonly sought for any clone, GenBank accession, or gene from human, mouse, rat.
http://source.stanford.edu

SVMHC - (Found June 19, 2008 )

SVMHC is a server for prediction of MHC class I and class II binding peptides. SVMHC can be used to find likely binders in a protein sequence and to investigate the effects of single nucleotide polymorphisms on MHC-peptide binding.
http://www-bs.informatik.uni-tuebingen.de/SVMHC/

TCAG: The Centre for Applied Genomics, Toronto - (Found June 19, 2008 )

The Centre for Applied Genomics is a Canadian centre for human genome and disease research. Resources include Genomic and cDNA library screening (human, mouse, dog, pig) provided free to Canadian academic researchers with a nominal clone retrieval fee. Also: Research Genetics, NIANIH and RIKEN cDNAs.
http://tcag.bioinfo.sickkids.on.ca/

TFBScluster - (Found June 19, 2008 )

TFBScluster is a web tool designed to identify clusters of transcription factor binding sites (TFBSs) conserved in mammalian and mouse genomes. By entering a specified range of TFBS, you can retrieve a list of SWISS-PROT characterized genes to which the clusters are localized.
http://hscl.cimr.cam.ac.uk/TFBScluster_genome_portal.html