biopython v1.71.0 Bio.SeqUtils.CheckSum

Functions to calculate assorted sequence checksums.

Link to this section Summary

Functions

Returns the crc32 checksum for a sequence (string or Seq object)

Returns the crc64 checksum for a sequence (string or Seq object)

Returns the GCG checksum (int) for a sequence (string or Seq object)

Returns the SEGUID (string) for a sequence (string or Seq object)

Link to this section Functions

Returns the crc32 checksum for a sequence (string or Seq object).

Note that the case is important:

 >>> crc32("ACGTACGTACGT")
 20049947
 >>> crc32("acgtACGTacgt")
 1688586483

Returns the crc64 checksum for a sequence (string or Seq object).

Note that the case is important:

 >>> crc64("ACGTACGTACGT")
 'CRC-C4FBB762C4A87EBD'
 >>> crc64("acgtACGTacgt")
 'CRC-DA4509DC64A87EBD'

Returns the GCG checksum (int) for a sequence (string or Seq object).

Given a nucleotide or amino-acid secuence (or any string), returns the GCG checksum (int). Checksum used by GCG program. seq type = str.

Based on BioPerl GCG_checksum. Adapted by Sebastian Bassi with the help of John Lenton, Pablo Ziliani, and Gabriel Genellina.

All sequences are converted to uppercase.

 >>> gcg("ACGTACGTACGT")
 5688
 >>> gcg("acgtACGTacgt")
 5688

Returns the SEGUID (string) for a sequence (string or Seq object).

Given a nucleotide or amino-acid secuence (or any string), returns the SEGUID string (A SEquence Globally Unique IDentifier). seq type = str.

Note that the case is not important:

 >>> seguid("ACGTACGTACGT")
 'If6HIvcnRSQDVNiAoefAzySc6i4'
 >>> seguid("acgtACGTacgt")
 'If6HIvcnRSQDVNiAoefAzySc6i4'

For more information about SEGUID, see: http://bioinformatics.anl.gov/seguid/ DOI: 10.1002/pmic.200600032