Ncbi Entrez

CopyCat is a handy application specially designed to offer users an easy and fast access to cophylogenetic analyses. It incorporates a wrapper for the program ParaFit, which conducts a statistical test for the presence of congruence between host and parasite phylogenies. CopyCat offers various... Platforms: Mac

Geneious Pro is an integrated, cross-platform bioinformatics software suite for manipulating, finding, sharing, and exploring biological data such as DNA sequences or proteins, phylogenies, 3D structure information, publications, etc. It features sequence alignment and phylogenetic analysis,... Platforms: Windows, Mac, Linux

CisPlusFinder predicts cis-regulatory modules based on perfect local ungapped sequences using comparative sequence data from multiple organisms. An overview of the CisPlusFinder can be found in the flowchart.tif file and is described in the following publication: Pierstorff, N., C.M. Bergman &... Platforms: Mac, BSD

DNAGalaxy is an attempt to produce an open-source bioinformatics software alternative to the expensive DNAStar Lasergene software. Its features currently include Blast and Entrez searching, a frontend to clustal and a sequence editor. It requires java1.5 Platforms: Windows, Mac, Linux

PerlPrimer is a free, open-source GUI application written in Perl that designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR) and sequencing. It aims to automate and simplify the process of primer design.PerlPrimer's current features include the following: - Calculation of... Platforms: *nix, Perl, BSD

BlastViewer provides an interactive graphical user interface for the analysis of the reports produced by the BLAST sequence database search system. BlastViewer is an easy to use software designed for everyday biological sequence analysis relying on BLAST. It allows an easy visualisation and... Platforms: Mac, Java 1.5 or later

NCBI has an implementation of BLAST algorithm on their website at www.ncbi.nlm.nih.gov/BLAST, which is good if you want to query short DNA or protein sequence against various sequence databases. The problem arises when large sequences need to be BLAST'ed against a sequence database or against... Platforms: Matlab

This demo illustrates a simple approach to perform taxonomy annotation of BLAST hits. It requires three taxonomy files gi_taxid_prot.dmp, names.dmp and nodes.dmp, which can be downloaded from the NCBI taxonomy FTP site. Platforms: Matlab

dbSNPtool starts a GUI to return polymorphism data from dbSNPwww.ncbi.nih.gov/SNP Calling dbsnptool start the GUI, SNP % records are returned based on keyword. Each result is presented in a % listbox, clicking on the entry loads the sequence into the sequence %viewer. Information is presenting... Platforms: Matlab

Estimate LDL cholesterol based on measured total cholesterol (TC), HDL, and triglycerides (TG).The function 'estimateLDL(TC, HDL, TG, InputUnits)' provides an estimate for the LDL cholesterol on measured total cholesterol (TC), HDL cholesterol, and triglycerides (TG).For most cases, the classical... Platforms: Matlab

The Bioinformatic Software Bench for Drupal allows for a rapid and secure deployment of bioinformatic software. The BLAST, InterProScan, SSAHA2 and annot8r software are provided by default and plugins for new software can be readily written. An innovative graphical user interface guides both... Platforms: PHP

ProtSeqFetch is software for generating artificial metagenomes. The program downloads protein sequences at the genera level directly from the National Center for Biotechnology Information (NCBI) or extracts them from a local copy of the NCBI NR ("non-redundant") database. A non-redundant... Platforms: Mac

UGENE is a free cross-platform genome analysis suite. It works perfectly on Windows, Mac OS or Linux and requires only a few clicks to install. Features: * Multiple sequence alignment using MUSCLE 3, KAlign, Clustal; * HMM profiles build and search, based on the source of HMMER 2 and HMMER... Platforms: Mac

This script uses the gene name field(s) in a table downloaded from the UCSC Genome Browser to add gene names to an existing SVS marker map saved in the DSM file format. Note: Though the following instructions specify downloading a table containing genes based on the Mar. 2006 (NCBI36/hg18) Human... Platforms: Mac