bioinformatics-databases

NCBI Gene (formerly Entrez) lets you access the wealth of information at NCBI.

Detection of regions of genomic sequences that are rich in the CpG pattern is important because such regions are resistant to methylation and tend to be associated with genes which are frequently switched on. EBI's EMBOSS can be used to find CpG islands in a nucleotide sequence.

 

OTHER SITES:

 

Pepinfo (EMBOSS)

Create a variety of plots that display different amino acid properties, such as hydropathy or charged residues, and their position in the sequence

Launch Pepinfo

Pepstats (EMBOSS)

Calculate properties of your protein such as molecular weight

Launch Pepstats

Pepwindow (EMBOSS)

Draw a hydropathy plot for your protein sequence

Launch Pepwindow

SAPS

Evaluate a wide variety of additional protein sequence properties

Launch SAPS

Cpgplot (EMBOSS)

Identify and plot CpG islands in nucleotide sequence(s)

Launch Cpgplot

Newcpgreport (EMBOSS)

Identify CpG islands in nucleotide sequence(s)

Launch Newcpgreport

Isochore (EMBOSS)

Plot isochores in DNA sequences

Launch Isochore

Dotmatcher (EMBOSS)

Draw a threshold dotplot of two sequences

Launch Dotmatcher

Dotpath (EMBOSS)

Draw a non-overlapping wordmatch dotplot of two sequences

Launch Dotpath

Dottup (EMBOSS)

Display a wordmatch dotplot of two sequences

Launch Dottup

Polydot (EMBOSS)

Draw dotplots for all-against-all comparison of a sequence set

Launch Polydot

CUTG is a codon usage database populated from other international DNA sequence databases. Find the sum of the codon use of an organism from a list of 23093 organisms (2004).

A B C D E F G H I J K L MN O P Q R S T U V W X Y Z

Chloroplast Mitochondrion Others (intials are not capital)

AUGUSTUS is a database for ab initio prediction of alternative transcripts. You can predict a gene in eukaryotic genomic sequences based on a generalized hidden Markov model.

web interface

accuracy results

download AUGUSTUS

data sets

predictions

references

EasyGene is a prokaryotic gene finder that ranks ORFs by statistical significance. Predict and statistically evaluate predicted prokaryotic open reading frames (ORFs).

Complexity is a web resource for the analysis of DNA sequence complexity. Search for low complexity regions in long sequences and estimate complexity of groups of aligned sequences.

BLogo is a tool for the visualization of a bias in biological sequences. It detects and displays statistically significant position-specific sequence bias with reduced background noise.

 

AGenDA is a gene-prediction tool that is based on cross-species sequence comparison. The software tools CHAOS and DIALIGN are used to align a pair of syntenic genomic sequences, e.g. from human and mouse. AGenDA searches for conserved splice sites and start/stop codons at the boundaries of identified sequence homologies in order to identify potential exons; these potential exons are then used to assemble entire gene models.

• AGT-SDP Automatic Generated Test-Set Database for Protein-Protein Docking

  AGT-SDP (Automatic Generated Test-Set Database for Protein-Protein Docking) provides test cases for evaluating and benchmarking protein-protein docking algorithms.

• AIM Automatic Image processing for Microarrays

  Automatic Image processing for Microarrays

• biodomws BioDOM WebService

  WebService for the BioDOM Library

• bpr bucket-pointer refinement construction algorithm of suffix arrays

  Bpr is an implementation of the 'bucket-pointer refinement' construction algorithm for suffix arrays

• decomp decomp

  Suppose you are given a DNA fragment of mass 1897.27 Dalton and no other information. What nucleotide combinations are there that lead to exactly this mass? Decomp helps you solve this and similar problems efficiently.

• GenDB Open Source genome annotation system

  The GenDB system is an open source genome annotation system developed at the Center for Genome Research at Bielefeld University.

• libfid Full-text Index Data structure Library

  The Full-text Index Data structure library, libfid for short, is a portable software library for accessing indexed data through a simple C interface. It implements, among others, functions for reading indexed data from files, and performing common operations such as fast string matching on these. Easy alphabet handling for mapping between printable and binary alphabets is integrated from the ground up. Currently, the enhanced suffix array is the only full-text index data structure supported. A very simplistic program for constructing enhanced suffix arrays is included. The library is freely available as source code under the terms of the GNU Lesser General Public License

• mkESA Enhanced Suffix Array construction tool

  mkESA is an open source program for constructing enhanced suffix arrays (ESAs) from biological sequence data. The program is based on our implementation of Manzini's lightweight Deep-Shallow algorithm, which can also utilize multiple CPUs/cores for some extra speed-up. The generated output is compatible to the output of mkvtree from the Vmatch package written by Stefan Kurtz. mkESA is freely available as source code under the terms of the GNU General Public License

• MoRAine

  MoRAine is a tool for the reannotation of transcription factor binding motifs and the creation of sequence logos.

• Paper2Sequence

  Simple retrieval of sequences

• PathAligner

  Metabolic Pathway Retrieval and Alignment

• Phase4

  Automatic evaluation of database search methods.

• stcdb Signal Transduction Classification Database
• Wotd Write-only top-down construction algorithm of suffix trees

  Wotd is an implementation of the ''lazy'' write-only top-down construction algorithm of suffix trees using a very space-efficient representation.

• XenDB Xenopus laevis EST database

  XenDB is a database of clustered EST and cDNA sequences from Xenopus laevis. ESTs are clustered by a suffix array-based approach and contig sequences compared to proteins from major model organisms. Cross species mapping functionality will be useful for researchers working on comparative genome analysis.