This software package for gene and protein identification, using sensitive, selective and rapid similarity searches of protein and nucleotide sequence databases.
ArrayExpress is a database of functional genomics experiments that can be queried and the data downloaded. It includes gene expression data from microarray and high throughput sequencing studies. Data is collected to MIAME and MINSEQE standards.
Biological Concept Diagram Editor (BCDE) is a conceptual relationship diagramming tool specifically designed for biomedical researchers. Compared to existing diagramming/drawing tools, BCDE has several advantages. It allows for efficient knowledge/data capture, fast diagram creation, easy data retrieval and flexible exporting.
BFAST facilitates the fast and accurate mapping of short reads to reference sequences…Specifically, BFAST was designed to facilitate whole-genome resequencing, where mapping billions of short reads with variants is of utmost importance.
how genes interact in dynamic graphical models.
Clustal Omega is a new multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments.
Dapple is a program for quantitating spots on a two-color DNA microarray image. Given a pair of images from a comparative hybridization, Dapple finds the individual spots on the image, evaluates their qualities, and quantifies their total fluorescent intensities.
Includes sequence alignment, rapid database searching with sequence patterns, protein motif identification, including domain analysis, nucleotide sequence pattern analysis,codon usage analysis for small genomes, rapid identification of sequence patterns in large scale sequence sets, and presentation tools for publication.
A program for phylogenetic footprinting. Phylogenetic footprinting is a method that identifies putative regulatory elements in DNA sequences. It identifies regions of DNA that are unusually well conserved across a set of orthologous sequences
GeneCards is a searchable, integrated database of human genes that provides comprehensive, updated, and user-friendly information on all known and predicted human genes.
…a hidden Markov model-based approach that can accurately pinpoint regions to where significantly more sequence reads map.
McPromoter is a program aiming at the exact localization of eukaryotic RNA polymerase II transcription start sites.
The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
Pick primers from a DNA sequence
T-Coffee is a multiple sequence alignment package. By using T-Coffee one can align sequences or to combine the output of your favorite alignment methods (Clustal, Mafft, Probcons, Muscle...) into one unique alignment (M-Coffee).
Using Zoom, zillions of short reads are mapped back to reference genomes, including post-analysis at unparalleled in speed, at full sensitivity.
Usefull HTML Tools
Important Useful Sites