MultiPipMaker: a comparative alignment server for multiple DNA sequences.

Curr Protoc Bioinformatics 2010 Jun;Chapter 10:Unit10.4

The Pennsylvania State University, University Park, Pennsylvania, USA.

The MultiPipMaker World Wide Web server (http://www.bx.psu.edu) provides a tool for aligning multiple DNA sequences and visualizing regions of conservation among them. This unit describes its use and gives an explanation of the resulting output files and supporting tools. Features provided by the server include alignment of up to 20 very long genomic sequences, output choices of a true, nucleotide-level multiple alignment and/or stacked, pairwise percent identity plots, and support for user-specified annotations of genomic features and arbitrary regions, with clickable links to additional information. Input sequences other than the reference can be fragmented, unordered, and unoriented.

Download full-text PDF

Source
http://dx.doi.org/10.1002/0471250953.bi1004s30DOI Listing
June 2010
11 Reads

Publication Analysis

Top Keywords

dna sequences
8
multiple dna
8
long genomic
4
alignment long
4
include alignment
4
genomic sequences
4
sequences output
4
output choices
4
regions clickable
4
explanation output
4
server include
4
tools features
4
supporting tools
4
files supporting
4
clickable links
4
features provided
4
choices true
4
provided server
4
links additional
4
true nucleotide-level
4

References

(Supplied by CrossRef)
Organization of human homeobox genes
Boncinelli et al.
Hum. Reprod. 1988
CpG islands in vertebrate genomes
Gardiner-Garden et al.
J. Mol. Biol. 1987
In vitro and transgenic analysis of a human HOXD4 retinoid-responsive enhancer
Morrison et al.
Development 1996

Pough et al.
1999

Similar Publications