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chain-format

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chain-format is a text data format created in 2013.

#3109on 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.


Example from the web:
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

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