MultiPipMaker: A Comparative Alignment Server for Multiple DNA Sequences
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- Abstract
- Table of Contents
- Figures
- Literature Cited
Abstract
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. Curr. Protoc. Bioinform. 30:10.4.1?10.4.14. © 2010 by John Wiley & Sons, Inc.
Keywords: multiple alignment; percent identity plot; genomic analysis; conserved non?coding sequences
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PDF or HTML at Wiley Online LibraryTable of Contents
- Introduction
- Strategic Planning
- Basic Protocol 1: MultiPipMaker: Multiple Alignment Server
- Support Protocol 1: Installing and Using Stand‐Alone refine and single_cov Programs
- Support Protocol 2: Using PipHelper to Prepare MultiPipMaker Input Files from Data in the UCSC Genome Browser
- Guidelines for Understanding Results
- Commentary
- Literature Cited
- Figures
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Figure 10.4.1 Flow chart outlining the steps for using MultiPipMaker. View Image -
Figure 10.4.2 Textual summary of a MultiPipMaker submission. This is returned as an acknowledgement page indicating that the job has been accepted, and is also included with the output. It lists the length of each sequence and displays a portion of the FASTA header line. It also gives information such as the options selected and the order of the sequences in the alignment. View Image -
Figure 10.4.3 Excerpt from the alignment of the paralogous HOX clusters in human. The HOXA4 locus is shown aligned to HOXB4 , HOXC4 , and HOXD4 . Each panel in the MultiPip represents a pairwise alignment to the HOXA reference sequence. The horizontal axis above the plots shows icons representing simple repeats (vertical bars), CpG islands (low rectangles), exons (numbered black boxes), the gene name, and the direction of transcription. The horizontal red and green bars at the very top are clickable annotation links (see text). Colored underlays within the plots represent annotations from the HOXA cluster; those in the top half of each panel include characterized promoter regions (pink), UTRs represented in the EST libraries (green), coding exons (red), introns (yellow), and annotated UTRs (light orange). Vertical bars in each bottom half represent experimentally characterized protein binding sites for AP2 (purple) and the RARE sequence (orange). The lower panel is an excerpt from a nucleotide‐level alignment in the region of the partly‐conserved RARE and non‐conserved AP2 transcription factor binding sites. Conserved nucleotides are shown as dots. View Image
Videos
Literature Cited
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| Key References | |
| Schwartz et al., 2000. See above. | |
| Describes the PipMaker server. PipMaker computes and displays pairwise alignments whereas MultiPipMaker computes and displays multiple sequence alignments. | |
| Schwartz et al., 2003a. See above. | |
| Describes the MultiPipMaker server and supporting tools. | |
| Internet Resources | |
| http://www.bx.psu.edu | |
| Links to alignment programs including PipMaker and MultiPipMaker, software, publications, example pages, and instructions for use of the tools and the server. | |
| http://genome.ucsc.edu | |
| Home page for the UCSC Genome Browser. | |
| http://www.adobe.com | |
| Home page for downloading Adobe Reader. | |
| http://www.gzip.org | |
| Home page for the GNUzip software package. | |
| http://www.ncbi.nlm.nih.gov/sites/entrez?db=nucleotide | |
| Entrez Nucleotide Web site containing sequenced DNA from numerous sources. | |
| http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene | |
| Entrez Gene Web site containing annotations of genes and links to related resources. | |
| http://www.ncbi.nlm.nih.gov/pubmed/ | |
| PubMed Web site: repository of published scientific literature. | |
| http://www.genome.gov/1005107 | |
| ENCODE Project homepage. Links to sequences and general information about the project. |
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