CHAIN File

What are CHAIN files and how to open them

Are you having problems opening a CHAIN file or are you simply curious about its contents? We're here to explain the properties of these files and provide you with software that can open or handle your CHAIN files.

What is a CHAIN file?

A .CHAIN file is a Chain Format file.

Chain Format files store pairwise sequence alignments between two genomes (a reference/target genome and a query genome) and allow gaps in both sequences. They are produced by the UCSC Genome Browser's alignment pipeline - specifically using tools such as axtChain - and are used for tasks like converting genome coordinates between different versions (e.g. LiftOver).

Each alignment consists of a header line followed by one or more alignment data lines, ending with a blank line. The header line begins with the keyword chain and then lists attributes: chain score; target chromosome name; target size; target strand; target start and end positions; query chromosome name; query size; query strand; query start and end positions; and a unique chain ID. The coordinates are zero-based and half-open (start inclusive, end exclusive) so that, for example, a block from positions 0 - 100 corresponds to the first 100 bases.

Following the header, each alignment data line describes an ungapped matching block and its spacing to the next block. They contain three fields: the size of the matching block; dt, the gap in the target sequence before the next block; dq, the gap in the query sequence before the next block. The final line in this section has only the size of the final matching block.

Files in this format start with the ASCII signature "chain" at the very beginning of the file (bytes 0x63 0x68 0x61 0x69 0x6E at offset 0).

How to open CHAIN files

Important: Different programs may use files with the CHAIN file extension for different purposes, so unless you are sure which format your CHAIN file is, you may need to try a few different programs.

We have not yet verified any programs for Windows that work with this specific file format. If you know one, please use the 'Suggest a program' link below. Thanks!

Last updated: August 31, 2026

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