UNM Office of Biocomputing's Genomics Home Page

Welcome to the Genomics Home Page at the UNM School of Medicine's Office of Biocomputing. This page contains links and information about various bioinformatics resources (software, databases, etc) developed and/or administrated by the Office of Biocomputing. These resources are made available by the Office of Biocomputing to support genomics-based research at UNM.

Please note: many of the links below are subject to access control restrictions. Most of the computational resources, for example, are available only to users within UNM.

Please send all comments, questions, etc. to Steve Mathias (smathias at poblano dot health dot unm dot edu).

Useful Links: Human Genome | Model Organisms

UNM Microarray Database System

Microarray Probe Annotator Application

Bioinformatics Resources and Tools

EMBOSS

The European Molecular Biology Open Software Suite (EMBOSS) (Rice et al., 2000) is a popular set of free software tools for sequence analysis and other related bioinformatics tasks. Traditionally, the EMBOSS applications are run from the command-line on a Unix-based computer system. In addition to the command line interface there are also several graphical interfaces to EMBOSS, one of which is EMBOSS-GUI, a web-based front end to EMBOSS developed and made available by Luke McCarthy. The Office of Biocomputing makes both the command-line and EMBOSS-GUI interfaces available to HSC researchers. If you would like command-line access to EMBOSS, please contact Steve Mathias (smathias at poblano dot health dot unm dot edu). EMBOSS-GUI may be accessed from any computer with a web browser via the link below. [EMBOSS Documentation] | [EMBOSS Tutorial] | [EMBOSS-GUI[ | [Intro to EMBOSS-GUI]

BLAST Searches

Web interfaces to the NCBI-BLAST suite of programs for sequence comparison.
[BLAST Programs | BLAST Databases | BLAST Manual]

Reactome

The Reactome project is a collaboration among Cold Spring Harbor Laboratory, The European Bioinformatics Institute, and The Gene Ontology Consortium to develop a curated resource of core pathways and reactions in human biology. The information in this database is authored by biological researchers with expertise in their field, maintained by the Reactome editorial staff, and cross-referenced with with PubMed, GO, and the sequence databases LocusLink, Ensembl and SwissProt. The OBC maintains a local installation of the Reactome software and database which may be accessed via the link below.
[ Reactome Home ]

GBrowse: Generic Genome Browser

GBrowse is a combination of database and interactive web page for manipulating and displaying annotations on genomes. GBrowse is made available by the Generic Model Organism Database Project.
[yeast | human | documentation]

siRNA Tool

This tool generates potential siRNA target sequences based on a set of input criteria, and performs BLAST searches to screen each of the target sequences. Results are made available as web page reports.
[siRNA Tool | documentation]