chain-format is a text data format created in 2013.
| #3111on PLDB | 11Years Old |
The chain format describes a pairwise alignment that allow gaps in both sequences simultaneously. Each set of chain alignments starts with a header line, contains one or more alignment data lines, and terminates with a blank line. The format is deliberately quite dense.
chain 4900 chrY 58368225 + 25985403 25985638 chr5 151006098 - 43257292 43257528 1
9 1 0
10 0 5
61 4 0
16 0 4
42 3 0
16 0 8
14 1 0
3 7 0
48
chain 4900 chrY 58368225 + 25985406 25985566 chr5 151006098 - 43549808 43549970 2
16 0 2
60 4 0
10 0 4
70