Latest Tools and Methods in Bioinformatics (2008).
Bioinformatics Softwares. Bioinformatics Tools.
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:
GeneChaser:
Identifying all biological and clinical conditions in which genes of interest are differentially expressed.
It is an automated approach to annotate and analyze all Gene Expression Omnibus (GEO) data sets, including 1,515 GEO data sets from 231 microarray types across 42 species, and performed 12,658 group versus group comparisons of 24 GEO-specified types. We then built GeneChaser, a web server that enables biologists and clinicians without bioinformatics skills to easily identify biological and clinical conditions in which a gene or set of genes was differentially expressed. GeneChaser displays these conditions in graphs, gives statistical comparisons, allows sort/filter functions and provides access to the original studies.
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).
WindowMasker:
window-based masker for sequenced genomes.
rHVDM:
An R package to predict the activity and targets of a transcription factor.
ATOM:
A Powerful Gene-Based Association Test by Combining Optimally Weighted Markers.
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.