What it does
This tool converts every MAF block to an interval line (in BED format; scroll down for description of MAF and BED formats) describing position of that alignment block within a corresponding genome.
The interface for this tool contains two pages (steps):
- Step 1 of 2. Choose multiple alignments from history to be converted to BED format.
- Step 2 of 2. Choose species from the alignment to be included in the output and specify how to deal with alignment blocks that lack one or more species:
- Choose species - the tool reads the alignment provided during Step 1 and generates a list of species contained within that alignment. Using checkboxes you can specify taxa to be included in the output (only reference genome, shown in bold, is selected by default). If you select more than one species, then more than one history item will be created.
- Choose to include/exclude blocks with missing species - if an alignment block does not contain any one of the species you selected within Choose species menu and this option is set to exclude blocks with missing species, then coordinates of such a block will not be included in the output (see Example 2 below).
Example 1: Include only reference genome (hg18 in this case) and include blocks with missing species:
For the following alignment:
a score=68686.000000 s hg18.chr20 56827368 75 + 62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- s panTro2.chr20 56528685 75 + 62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- s rheMac2.chr10 89144112 69 - 94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA------- s mm8.chr2 173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC------- s canFam2.chr24 46551822 67 + 50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C a score=10289.000000 s hg18.chr20 56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG s panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG s rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG
the tool will create a single history item containing the following (note that field 4 is added to the output and is numbered iteratively: hg18_0, hg18_1 etc.):
chr20 56827368 56827443 hg18_0 0 + chr20 56827443 56827480 hg18_1 0 +
Example 2: Include hg18 and mm8 and exclude blocks with missing species:
For the following alignment:
a score=68686.000000 s hg18.chr20 56827368 75 + 62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- s panTro2.chr20 56528685 75 + 62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- s rheMac2.chr10 89144112 69 - 94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA------- s mm8.chr2 173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC------- s canFam2.chr24 46551822 67 + 50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C a score=10289.000000 s hg18.chr20 56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG s panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG s rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG
the tool will create two history items (one for hg18 and one fopr mm8) containing the following (note that both history items contain only one line describing the first alignment block. The second MAF block is not included in the output because it does not contain mm8):
History item 1 (for hg18):
chr20 56827368 56827443 hg18_0 0 +
History item 2 (for mm8):
chr2 173910832 173910893 mm8_0 0 +
About formats
MAF format multiple alignment format file. This format stores multiple alignments at the DNA level between entire genomes.
- The .maf format is line-oriented. Each multiple alignment ends with a blank line.
- Each sequence in an alignment is on a single line.
- Lines starting with # are considered to be comments.
- Each multiple alignment is in a separate paragraph that begins with an "a" line and contains an "s" line for each sequence in the multiple alignment.
- Some MAF files may contain two optional line types:
- An "i" line containing information about what is in the aligned species DNA before and after the immediately preceding "s" line;
- An "e" line containing information about the size of the gap between the alignments that span the current block.
BED format Browser Extensible Data format was designed at UCSC for displaying data tracks in the Genome Browser. It has three required fields and a number of additional optional ones:
The first three BED fields (required) are:
1. chrom - The name of the chromosome (e.g. chr1, chrY_random). 2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.) 3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval).
Additional (optional) fields are:
4. name - The name of the BED line. 5. score - A score between 0 and 1000. 6. strand - Defines the strand - either '+' or '-'.