Genome Environment Browser (GEB):

Repeat elements and other non-genic sequence features at a given chromosomal locus, here defined as the genome environment, It is a dynamic browser for visualising high-throughput experimental data in the context of genome features.

UCSC Genome Browser tutorial:

REannotate:

A computational tool to process RepeatMasker annotation for automated i) defragmentation of dispersed repetitive elements, ii) resolution of the temporal order of insertions in clusters of nested elements, and iii) estimating the age of the elements, if they have long terminal repeats.

FastMap:

Fast eQTL Mapping in Homozygous Populations.

AnEnPi:

Identification and annotation of analogous enzymes.

ReRep:

computational detection of repetitive sequences in genome survey sequences (GSS).

rHVDM:

An R package to predict the activity and targets of a transcription factor

PASTAA:

Identifying transcription factors associated with sets of co-regulated genes.

ARCS-Motif:

Discovering Correlated Motifs from Unaligned Biological Sequences.

ASTD:

The Alternative Splicing and Transcript Diversity database.

SELECTpro:

Effective protein model selection using a structure-based energy function resistant to BLUNDERs.

I-TASSER:

Server for protein 3D structure prediction

BayesMD:

Flexible biological modeling for motif discovery.

MFEprimer:

Multiple factor evaluation of the specificity of PCR primers.