WO1999001940A1 - Biological data - Google Patents
Biological data Download PDFInfo
- Publication number
- WO1999001940A1 WO1999001940A1 PCT/GB1998/001937 GB9801937W WO9901940A1 WO 1999001940 A1 WO1999001940 A1 WO 1999001940A1 GB 9801937 W GB9801937 W GB 9801937W WO 9901940 A1 WO9901940 A1 WO 9901940A1
- Authority
- WO
- WIPO (PCT)
- Prior art keywords
- sequence data
- bits
- monomer
- datatype
- biological sequence
- Prior art date
Links
Classifications
-
- H—ELECTRICITY
- H03—ELECTRONIC CIRCUITRY
- H03M—CODING; DECODING; CODE CONVERSION IN GENERAL
- H03M7/00—Conversion of a code where information is represented by a given sequence or number of digits to a code where the same, similar or subset of information is represented by a different sequence or number of digits
- H03M7/30—Compression; Expansion; Suppression of unnecessary data, e.g. redundancy reduction
Definitions
- This invention relates to the compression of biological sequence data for electronic storage.
- Bio sequence data is typically represented in an alphabetic manner, rather than by chemical formula, with each letter representing a monomer unit in a biological polymer (Table I).
- DNA sequences are represented as strings of letters chosen from a simple four-letter "alphabet".
- Each A, C, G or T represents a monomer unit (nucleotide) in a DNA polymer.
- proteins are made up of twenty different monomer units (amino acids), which have each been assigned single letter codes.
- Alphabetic text-based computer information is generally stored and manipulated using the char datatype, using 8 bits (1 byte) and a conventional file of biological sequence data is made up of a string of characters of datatype char.
- a conventional file of sequence data uses a single byte to represent each monomer, so the amino acid sequence of the glycogen synthase protein, for example, requires 737 bytes of storage using the one-letter amino acid code, and the corresponding DNA sequence requires 2211 bytes.
- the char datatype was designed for representing a full character set, including upper and lower case letters plus numbers, punctuation, and other characters, and each 8-bit char can represent 256 (2 8 ) different values. Using the char datatype and alphanumeric characters to store DNA sequences therefore fails to utilise 252 of the available values. Similarly, protein sequences waste 236 values. Other datatypes which are in common usage for data storage include int (16 bits), long (32 bits), 7o ⁇ t (32 bits), although this may vary from machine to machine.
- the DNA and RNA alphabets each consist of 4 letters and, rather than storing these sequences in alphanumeric form using strings of char datatype, using a sub-byte datatype would enable a significant storage saving. Degenerate nucleic acid sequence information (which can be represented using a 16 letter alphabet) and protein sequences could also be treated in this way. It would therefore be useful to define a sub-byte datatype in order to take advantage of the small size of the biological alphabet.
- the commonly used blast sequence comparison program converts single byte char data into a half-byte working space whilst manipulating data. This is a temporary measure, however, and data is not stored in this manner using a specific sub-byte datatype.
- the invention is based upon the realisation that using a whole byte to represent a monomer in a biological sequence is not the most efficient means of permanent storage.
- a sub-byte datatype for the storage or manipulation of biological sequence data in a programming language or a database.
- the invention also provides a programming language or a database which utilises a sub-byte datatype for the storage or manipulation of biological sequence data.
- sub-byte it is meant fewer than 8 bits.
- the datatype may be intrinsic to a program or programming language, or it may be user-defined.
- the invention is not limited, however, to situations where a formal datatype must be defined.
- a computer program which stores biological sequence data using fewer than 8 bits to represent each monomer in said sequence data.
- the invention also provides a file containing biological sequence data, wherein each monomer in said sequence data is represented using fewer than 8 bits.
- a method for compressing biological sequence data comprising representing each monomer in said sequence data by using fewer than 8 bits.
- the invention also provides a method for reducing the size of a file in which biological sequence data is represented using 8 or more bits per monomer, comprising replacing the representation of each monomer with a representation using fewer than 8 bits.
- a computer programmed to store biological sequence data by using fewer than 8 bits to represent each monomer in said sequence data.
- a computer comprising means for alphabetic entry of biological sequence data, means to convert said sequence data into a format wherein each monomer unit is represented using fewer than 8 bits and, preferably, means to store said data.
- a storage medium holding biological sequence data, wherein said sequence data is stored using fewer than 8 bits to represent each monomer in said sequence data.
- the storage medium may be in any appropriate form, such as a floppy disk, a CD-ROM, or a fixed disk drive.
- a method for transmitting biological sequence data comprising compressing the data by representing each monomer in said sequence data by using fewer than 8 bits before transmission, for instance over a network.
- biological sequence data which has been electronically stored using less than 8 bits to represent each monomer in said sequence data.
- the biological sequence data may be of any suitable kind, such as DNA sequence, RNA sequence, and protein or polypeptide sequence.
- nucleic acid sequences can be represented using 2 bits to represent each monomer (nucleotides A, C, G, or T U). Accordingly, a 2 bit datatype may be defined according to the invention for the storage or manipulation of nucleic acid sequences. Such a datatype is referred to herein as base.
- each nucleotide in a nucleic acid sequence By representing each nucleotide in a nucleic acid sequence by using only 2 bits, 4 nucleotides can be stored in a single byte. This represents a 75% compression compared with the conventional representation of each nucleotide using a single byte.
- nucleic acid sequence is not definite, more than 2 bits are required to represent each nucleotide.
- N is used according to IUPAC convention.
- the alphabet of this IUPAC convention (Table I) has 16 members. This can be conveniently represented using 4 bits per member. Accordingly, a 4 bit datatype may be defined according to the invention for the storage or manipulation of degenerate or uncertain nucleic acid sequences. Such a datatype is referred to herein as longbase.
- nucleotide By representing each nucleotide in a sequence by using 4 bits, 2 nucleotides can be stored in a single byte. This represents a 50% compression compared with the conventional representation of each nucleotide using a single byte.
- each amino acid in a protein sequence By representing each amino acid in a protein sequence by using 6 bits, 4 amino acids can be stored in 3 bytes. This represents a 25% compression compared with the conventional representation of each amino acid using a single byte.
- the degree of degeneracy incorporated into a 6-bit representation or datatype also allows an amino acid to be represented in terms of codons, of which there are 64.
- a datatype used in this way is referred to herein as codon.
- Each single codon value represents a single codon, which inherently also defines an amino acid.
- the codon datatype represents three base entries, just as a codon is made up of three nucleotides.
- 4 codons can be represented in 3 bytes. This represents a 75% compression compared with the conventional representation of each codon using 3 bytes. It will also be appreciated that a full byte could be used to represent each codon, which would allow a degree of degeneracy and would represent a 67% compression compared with using 3 bytes to represent each codon.
- the various datatypes and compressions described above may not be suitable in all circumstances.
- the programming language C requires a string to have a NULL terminator. This is not possible with the base datatype, for instance, because all of the 4 possible values (permutations of 2 bits) are used to represent information, which does not allow a terminator to be represented.
- the IUPAC convention uses 15 representations for a DNA or RNA sequence, which does allow the sixteenth permutation to represent a terminator. In certain circumstances, however, a value may be needed to represent a gap (representing an unknown sequence of unknown length) which would remove the possibility of having a terminator.
- the codon datatype is also "full" since each of the 64 available values represents a codon.
- B represents asparagine or aspartate ie. N or D
- Z represents glutamine or glutamate ie.
Landscapes
- Engineering & Computer Science (AREA)
- Theoretical Computer Science (AREA)
- Information Retrieval, Db Structures And Fs Structures Therefor (AREA)
Abstract
Description
Claims
Priority Applications (3)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
EP98932338A EP0995271A1 (en) | 1997-07-01 | 1998-07-01 | Biological data |
AU82278/98A AU8227898A (en) | 1997-07-01 | 1998-07-01 | Biological data |
JP50665999A JP2002508130A (en) | 1997-07-01 | 1998-07-01 | Biological data |
Applications Claiming Priority (2)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
GB9713921.6 | 1997-07-01 | ||
GBGB9713921.6A GB9713921D0 (en) | 1997-07-01 | 1997-07-01 | Biological data |
Publications (1)
Publication Number | Publication Date |
---|---|
WO1999001940A1 true WO1999001940A1 (en) | 1999-01-14 |
Family
ID=10815230
Family Applications (1)
Application Number | Title | Priority Date | Filing Date |
---|---|---|---|
PCT/GB1998/001937 WO1999001940A1 (en) | 1997-07-01 | 1998-07-01 | Biological data |
Country Status (5)
Country | Link |
---|---|
EP (1) | EP0995271A1 (en) |
JP (1) | JP2002508130A (en) |
AU (1) | AU8227898A (en) |
GB (1) | GB9713921D0 (en) |
WO (1) | WO1999001940A1 (en) |
Cited By (5)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
EP1313225A1 (en) * | 2000-04-19 | 2003-05-21 | Satoshi Omori | Nucleotide sequence information, and method and device for recording information on sequence of amino acid |
EP1443449A2 (en) * | 2003-02-03 | 2004-08-04 | Samsung Electronics Co., Ltd. | Apparatus, method and computer readable medium for encoding a DNA sequence |
US6912469B1 (en) * | 2000-05-05 | 2005-06-28 | Kenneth J. Cool | Electronic hybridization assay and sequence analysis |
US20090298702A1 (en) * | 2008-06-02 | 2009-12-03 | Xing Su | Nucleic acid sequencing using a compacted coding technique |
US10790044B2 (en) * | 2016-05-19 | 2020-09-29 | Seven Bridges Genomics Inc. | Systems and methods for sequence encoding, storage, and compression |
Citations (2)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US4701744A (en) * | 1986-03-27 | 1987-10-20 | Rca Corporation | Method and apparatus for compacting and de-compacting text characters |
WO1997031327A1 (en) * | 1996-02-26 | 1997-08-28 | Motorola Inc. | Personal human genome card and methods and systems for producing same |
-
1997
- 1997-07-01 GB GBGB9713921.6A patent/GB9713921D0/en active Pending
-
1998
- 1998-07-01 EP EP98932338A patent/EP0995271A1/en not_active Withdrawn
- 1998-07-01 WO PCT/GB1998/001937 patent/WO1999001940A1/en not_active Application Discontinuation
- 1998-07-01 JP JP50665999A patent/JP2002508130A/en active Pending
- 1998-07-01 AU AU82278/98A patent/AU8227898A/en not_active Abandoned
Patent Citations (2)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US4701744A (en) * | 1986-03-27 | 1987-10-20 | Rca Corporation | Method and apparatus for compacting and de-compacting text characters |
WO1997031327A1 (en) * | 1996-02-26 | 1997-08-28 | Motorola Inc. | Personal human genome card and methods and systems for producing same |
Cited By (9)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
EP1313225A1 (en) * | 2000-04-19 | 2003-05-21 | Satoshi Omori | Nucleotide sequence information, and method and device for recording information on sequence of amino acid |
EP1313225A4 (en) * | 2000-04-19 | 2003-05-21 | Satoshi Omori | Nucleotide sequence information, and method and device for recording information on sequence of amino acid |
US6912469B1 (en) * | 2000-05-05 | 2005-06-28 | Kenneth J. Cool | Electronic hybridization assay and sequence analysis |
EP1443449A2 (en) * | 2003-02-03 | 2004-08-04 | Samsung Electronics Co., Ltd. | Apparatus, method and computer readable medium for encoding a DNA sequence |
EP1443449A3 (en) * | 2003-02-03 | 2006-02-22 | Samsung Electronics Co., Ltd. | Apparatus, method and computer readable medium for encoding a DNA sequence |
US20090298702A1 (en) * | 2008-06-02 | 2009-12-03 | Xing Su | Nucleic acid sequencing using a compacted coding technique |
US8498824B2 (en) * | 2008-06-02 | 2013-07-30 | Intel Corporation | Nucleic acid sequencing using a compacted coding technique |
US10790044B2 (en) * | 2016-05-19 | 2020-09-29 | Seven Bridges Genomics Inc. | Systems and methods for sequence encoding, storage, and compression |
US20210050074A1 (en) * | 2016-05-19 | 2021-02-18 | Vladimir Semenyuk | Systems and methods for sequence encoding, storage, and compression |
Also Published As
Publication number | Publication date |
---|---|
JP2002508130A (en) | 2002-03-12 |
EP0995271A1 (en) | 2000-04-26 |
AU8227898A (en) | 1999-01-25 |
GB9713921D0 (en) | 1997-09-03 |
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