Bioinformatics Links Directory : Mapping and Assembly

This section contains links to mapping data, contig assembly, and genome resources used by many genome sequencing projects.

CAP3 Sequence Assembly Program - (Found July 2, 2008 )

Web-based contig assembly.
http://bioweb.pasteur.fr/seqanal/interfaces/cap3.html

EGassembler - (Found July 2, 2008 )

EGassembler is a pipeline for clustering and assembling sequence fragments from transcript (EST) data or from shotgun sequencing.
http://egassembler.hgc.jp

ESTpass - (Found July 2, 2008 )

ESTpass is a server for processing and annotating sequence data from expressed sequence tag (EST) projects.
http://estpass.kobic.re.kr/index.jsp

FPC - (Found July 2, 2008 )

FPC is a tool to assemble contigs from a set of clones and their restriction fragments.
http://www.genome.arizona.edu/software/fpc/

NCBI Clone Registry - (Found July 2, 2008 )

A database that integrates information about genomic clones and libraries, including sequence data, genomic position, and distributor information.
http://www.ncbi.nlm.nih.gov/genome/clone/

PhredPhrapConsed System - (Found July 2, 2008 )

UNIX-based, base-calling, sequence assembly and finishing tools used by most genome sequence centres; free for non-commercial use.
http://www.phrap.org/

Projector 2 - (Found July 2, 2008 )

Projector 2 allows users to map completed portions of the genome sequence of an organism onto the finished (or unfinished) genome of a closely-related species or strain. Using the related genome sequence as a template can facilitate sequence assembly and the sequencing of the remaining gaps.
http://molgen.biol.rug.nl/websoftware/projector2/

PromoSer - (Found July 2, 2008 )

Server which aims to extract proximal promoter sequences from mammalian genomes. Does so by mapping mRNA and EST sequences and tracking overlapping alignments to find the transcription start site.
http://biowulf.bu.edu/zlab/PromoSer/

Staden Package - (Found July 2, 2008 )

UNIX-based tools for sequence assembly, mutation detection and sequence analysis; free for non-commercial use. Note that Staden development and support have ceased due to lack of funding, despite widespread use.
http://www.mrc-lmb.cam.ac.uk/pubseq/