For a complete definition of all fields while in the twoBit structure, see this description within the source code.
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HAL is usually a graph-dependent composition to efficiently keep and index a number of genome alignments and ancestral reconstructions. HAL documents are represented in HDF5 format, an open regular for storing and indexing substantial, compressed scientific info sets. Genomes inside of HAL are structured according to the phylogenetic tree that relate them: Just about every genome is segmented into pairwise DNA alignment blocks with respect to its father or mother and youngsters (if existing) during the tree. Observe that When the phylogeny is unfamiliar, a star tree can be employed.
The position characters is usually one among the next values: C -- the sequence before or soon after is contiguous using this block.
UCSC. This causes it to be probable to Screen alignments from documents which are so substantial that the relationship to UCSC would day out when trying to upload The complete file to UCSC. Equally the BAM file and its involved index file keep on being on the Website-obtainable server (http or ftp), not to the UCSC server.
position -- A personality that specifies the connection between the non-aligning sequence On this block and the sequence that appears in the past and subsequent blocks.
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The "e" strains reveal that There's not aligning DNA to get a species but that The present block is bridged by a sequence that connects blocks in advance of and after this block. The next fields are defined by posture rather then identify=worth pairs.
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