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Stitch MAF blocks (version 1.0.1)

Choose intervals:

MAF Source:

MAF Type:

Choose species:

Select species to be included in the final alignment

Split into Gapless MAF blocks:

When set to Yes, blocks are divided around gaps appearing in any species. This will prevent gaps occurring in the interior of the sequence for an aligning species from overwriting a nucleotide found for the same position in a lower-scoring block.

What it does

A single genomic region can be covered by multiple alignment blocks. In many cases it is desirable to stitch these alignment blocks together. This tool accepts a list of genomic intervals. For every interval it performs the following:

finds all MAF blocks that overlap the interval;

sorts MAF blocks by alignment score;

stitches blocks together and resolves overlaps based on alignment score;

outputs alignments in FASTA format.

Example

Here three MAF blocks overlapping a single interval are stitched together. Space between blocks 2 and 3 is filled with gaps:

/repository/static/images/653328721ad4f0db/images%2Fmaf_icons%2FstitchMaf.png