Description

This track represents the alignments of the fosmid library ABC10 (NA19240).

Display convention

A clone pair alignment is represented as two thick blocks (end sequence alignment) connected by a line (insert) with arrows indicating the direction of alignment. Alignments are categorized into the following sub-tracks:
The following color key is used:

Methods

ABC10 end sequences were mapped using MEGABLAST (similarity=0.99, parameters: -D 2 -v 7 -b 7 -e 1e-40 -p 80 -s 90 -W 12 -t 21 -F F) to a repeat-masked genome assembly (parameters: -e wublast -xsmall -no_is -s -species Homo sapiens). Expected insert size for fosmids was set to (min) 32 Kbp and (max) 48 Kbp. Resulting clone alignments were grouped into the following categories based on uniqueness of the alignment for a given pair of clones, alignment orientation and the inferred insert size from the assembly.

Credits

Please feel free to contact Mitchell Vollger or Evan Eichler with any questions and/or concerns regarding this or other tracks. Thanks to Shwetha Canchi Murali from UW for generating the alignments.

References

Zhang Z, Schwartz S, Wagner L, Miller W. A greedy algorithm for aligning DNA sequences. J Comput Biol. 2000;7(1-2):203-214. PMID: 10890397.

A Smith, R Hubley, P Green - RepeatMasker Open-4.0, 2013