Sequence Analysis

Sequence Analysis project is a collage of coding projects which I have written over the past several years for various clients in my work as a bioinformatics consultant. These clients have graciously allowed me to release these works into the public domain as freeware for Macintosh OS X in... Platforms: *nix

POSA (Perl Objects for Sequence Analysis) provides an easy-to-use perl interface to handling raw ABI sequence trace files. For example: fasta can be extracted, sequence contigs can be build and putative SNPs and SBE primers can be easily generated. Platforms: Windows, Mac, Linux

Oligomer is a small, simple, Java based application specially designed to help you perform sequence analysis with standard and mixed bases. This tool will also help you find out the physical properties of the sequence, so that you get a complete bio-informatics software. for WindowsAll Platforms: Windows

ParsInsert efficiently produces both a phylogenetic tree and taxonomic classification for sequences for microbial community sequence analysis. This is a C++ implementation of the Parsimonious Insertion algorithm. Platforms: *nix

The goal of BioX is to bring easy-to-use sequence analysis to Mac-using biologists. It features graphical editors for sequences and multiple alignments, and supports opening and saving of many different sequence file formats. Analysis functions currently include searching for primers, restriction... Platforms: Mac

An automatically-updating library of genomic and genetic data; that provides a fully integrated, visually-advanced toolset for - Sequence alignment and phylogenetics - Sequence analysis, Contig assembly, - primers, restriction analysis - BLAST. Protein structure viewing, NCBI, UniProt, Pubmed... Platforms: Mac

A Molecular Biology software that provides tools with an intuitive interface to assists you in DNA cloning, sequence analysis and visualization. Serial Cloner 2.1 handles Features/Annotations and now allows to define, import and export, customized lists of Features. User can annotate any sequence... Platforms: Mac

A bioinformatics program for advanced RNA sequence analysis. All analyses are fully integrated in one single, user-friendly, and intuitive software application. Some analyses are: - Secondary structure prediction - Graphical view and editing of secondary structure - Tabular view of structures... Platforms: Mac

GATA is a graphic alignment tool for comparative sequence analysis. It makes use of BLAST to graphically align two DNA sequences, creating box- line- box representations of window scored local alignments. GATA also displays extensive GFF gene annotation. Platforms: Windows, Mac, Linux

IISA - Intelligent Interface to Sequence Analysis is an expert system for biological sequence analysis using Bioperl and Prolog. Platforms: Windows, Mac, Linux

pygr is a bioinformatics toolkit for sequence analysis and comparative genomics. pygr is highly scalable (e.g. one can easily query multi-genome alignments) and easy to use. Please see our new project page and wiki at http://code.google.com/p/pygr. Platforms: Windows, Mac, Linux

wEMBOSS is a web interface for the EMBOSS software package for biological sequence analysis. Under wEMBOSS each user has a private workspace where he can organize his work by creating projects and save results for later easy recovery and review. Platforms: *nix

Short Sequence Location Mapper loads the sequences, then aligns them and finally graphs and tables can be generated for one or more datasets at the same time. SSLM typically works with a BLAST data output file of short Solexa reads mapped to RNA subjects (for example pre-miRNA sequences). The... Platforms: Windows

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

The FastPCR software was developed to be an integrated tools environment that provides comprehensive facilities for designing primers for most PCR applications including standard, long distance, inverse, real-time, multiplex, unique and group-specific; overlap extension PCR (OE-PCR)... Platforms: Windows, XP, 2003, Windows Vista, XPX64, 7, 7x64

EMBOSS is "The European Molecular Biology Open Software Suite", it is a free Open Source software analysis package specially developed for the needs of the molecular biology user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of... Platforms: Most OSs

BioJava is a tool that includes objects for manipulating biological sequences and file parsers. It also features a DAS client and server support, access to BioSQL and Ensembl databases, tools for making sequence analysis GUIs and powerful analysis and statistical routines including a dynamic... Platforms: Windows

Seqlib is a Python module and application package for population genetics (and more). It allows processing, analyzing and simulating biological sequences. It is specifically designed for automated large-scale sequence analysis. Main features: * Fasta-centered input and output, format... Platforms: Mac

EnzymeX is a program for molecular biologists, developed to help you determine which restriction enzymes you should use to cut your DNA of interest. It now is a complete DNA sequence analysis and editing program, which contains powerful and unique features and is above all user friendly. Never... Platforms: Mac

Have you ever gotten frustrated with your DNA sequence analysis program because it didn't do a few things that you needed it to? Now, if you can code (or convince someone else to code for you), you can make 4Peaks go that extra distance for you. By making a plugin, you can get 4Peaks to send your... Platforms: Mac