MultiPipMaker and supporting tools -- alignments and analysis of multiple genomic DNA sequences
What you can do:
Align multiple, long genomic DNA sequences quickly and with good sensitivity.
Highlights:
- Alignments are computed between a contiguous reference sequence and one or more secondary sequences, which can be finished or draft sequence.
- The outputs include a stacked set of percent identity plots, called a MultiPip, comparing the reference sequence with subsequent sequences, and a nucleotide-level multiple alignment.
- New tools are provided to search MultiPipMaker output for conserved matches to a user-specified pattern and for conserved matches to position weight matrices that describe transcription factor binding sites (singly and in clusters).
Keywords:
- sequence alignment tool
- multiple sequence alignment tool
- DNA sequence alignment tool
- genomic sequence alignment tool
- comparative genomics tool
- gene prediction tool
- repetitive sequence prediction tool
- transcription factor binding site prediction tool
- cis-elements prediction tool
- cis-regulatory elements prediction tool
- DNA sequence analysis tool
- promoter analysis tool
- promoter elements prediction tool
Literature & Tutorials:
This record last updated: 06-14-2005