SYNOPSIS

ncbi-seg sequence [ W ] [ K(1) ] [ K(2) ] [ -x ] [ options ]

DESCRIPTION

ncbi-seg divides sequences into contrasting segments of low-complexity and high-complexity. Low-complexity segments defined by the algorithm represent ``simple sequences'' or ``compositionally-biased regions''.

Locally-optimized low-complexity segments are produced at defined levels of stringency, based on formal definitions of local compositional complexity (Wootton & Federhen, 1993). The segment lengths and the number of segments per sequence are determined automatically by the algorithm.

The input is a FASTA-formatted sequence file, or a database file containing many FASTA-formatted sequences. ncbi-seg is tuned for amino acid sequences. For nucleotide sequences, see EXAMPLES OF PARAMETER SETS below.

The stringency of the search for low-complexity segments is determined by three user-defined parameters, trigger window length [ W ], trigger complexity [ K(1) ] and extension complexity [ K(2)] (see below under PARAMETERS ). The defaults provided are suitable for low-complexity masking of database search query sequences [ -x option required, see below].

OUTPUTS AND APPLICATIONS

(1) Readable segmented sequence [Default]. Regions of contrasting complexity are displayed in ``tree format''. See EXAMPLES.

(2) Low-complexity masking (see Altschul et al, 1994). Produce a masked FASTA-formatted file, ready for input as a query sequence for database search programs such as BLAST or FASTA. The amino acids in low-complexity regions are replaced with ``x'' characters [-x option]. See EXAMPLES.

(3) Database construction. Produce FASTA-formatted files containing low-complexity segments [-l option], or high-complexity segments [-h option], or both [-a option]. Each segment is a separate sequence entry with an informative header line.

ALGORITHM

The SEG algorithm has two stages. First, identification of approximate raw segments of low- complexity; second local optimization.

At the first stage, the stringency and resolution of the search for low-complexity segments is determined by the W, K(1) and K(2) parameters. All trigger windows are defined, including overlapping windows, of length W and complexity less than or equal to K(1). ``Complexity'' here is defined by equation (3) of Wootton & Federhen (1993). Each trigger window is then extended into a contig in both directions by merging with extension windows, which are overlapping windows of length W and complexity less than or equal to K(2). Each contig is a raw segment.

At the second stage, each raw segment is reduced to a single optimal low-complexity segment, which may be the entire raw segment but is usually a subsequence. The optimal subsequence has the lowest value of the probability P(0) (equation (5) of Wootton & Federhen, 1993).

PARAMETERS

These three numeric parameters are in obligatory order after the sequence file name.

Trigger window length [ W ]. An integer greater than zero [ Default 12 ].

Trigger complexity. [ K1 ]. The maximum complexity of a trigger window in units of bits. K1 must be equal to or greater than zero. The maximum value is 4.322 (log[base 2]20) for amino acid sequences [ Default 2.2 ].

Extension complexity [ K2 ]. The maximum complexity of an extension window in units of bits. Only values greater than K1 are effective in extending triggered windows. Range of possible values is as for K1 [ Default 2.5 ].

OPTIONS

The following options may be placed in any order in the command line after the W, K1 and K2 parameters:

-a

Output both low-complexity and high-complexity segments in a FASTA-formatted file, as a set of separate entries with header lines.

-c [characters-per-line]

Number of sequence characters per line of output [Default 60]. Other characters, such as residue numbers, are additional.

-h

Output only the high-complexity segments in a FASTA-formatted file, as a set of separate entries with header lines.

-l

Output only the low-complexity segments in a FASTA-formatted file, as a set of separate entries with header lines.

-m [length]

Minimum length in residues for a high-complexity segment [default 0]. Shorter segments are merged with adjacent low-complexity segments.

-o

Show all overlapping, independently-triggered low-complexity segments [these are merged by default].

-q

Produce an output format with the sequence in a numbered block with markings to assist residue counting. The low-complexity and high-complexity segments are in lower- and upper-case characters respectively.

-t [length]

``Maximum trim length'' parameter [default 100]. This controls the search space (and search time) during the optimization of raw segments (see ALGORITHM above). By default, subsequences 100 or more residues shorter than the raw segment are omitted from the search. This parameter may be increased to give a more extensive search if raw segments are longer than 100 residues.

-x

The masking option for amino acid sequences. Each input sequence is represented by a single output sequence in FASTA-format with low-complexity regions replaced by strings of ``x'' characters.

EXAMPLES OF PARAMETER SETS

Default parameters are given by 'ncbi-seg sequence' (equivalent to 'ncbi-seg sequence 12 2.2 2.5'). These parameters are appropriate for low- complexity masking of many amino acid sequences [with -x option ].

Database-database comparisons:

More stringent (lower) complexity parameters are suitable when masked sequences are compared with masked sequences. For example, for BLAST or FASTA searches that compare two amino acid sequence databases, the following masking may be applied to both databases:

  ncbi-seg database 12 1.8 2.0 -x

Homopolymer analysis:

To examine all homopolymeric subsequences of length (for example) 7 or greater:

  ncbi-seg sequence 7 0 0

Non-globular regions of protein sequences:

Many long non-globular domains may be diagnosed at longer window lengths, typically:

  ncbi-seg sequence 45 3.4 3.75

For some shorter non-globular domains, the following set is appropriate:

  ncbi-seg sequence 25 3.0 3.3

Nucleotide sequences:

The maximum value of the complexity parameters is 2 (log[base 2]4). For masking, the following is approximately equivalent in effect to the default parameters for amino acid sequences:

  ncbi-seg sequence.na 21 1.4 1.6

EXAMPLES

The following is a file named 'prion' in FASTA format:

 >PRIO_HUMAN MAJOR PRION PROTEIN PRECURSOR
 MANLGCWMLVLFVATWSDLGLCKKRPKPGGWNTGGSRYPGQGSPGGNRYPPQGGGGWGQP
 HGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQGGGTHSQWNKPSKPKTNMKHMAGAAAAGA
 VVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCV
 NITIKQHTVTTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYQRGSSMVLFSSPPV
 ILLISFLIFLIVG

The command line:

 ncbi-seg /usr/share/doc/ncbi-seg/examples/prion.fa

gives the standard output below

 >PRIO_HUMAN MAJOR PRION PROTEIN PRECURSOR
                                   1-49   MANLGCWMLVLFVATWSDLGLCKKRPKPGG
                                          WNTGGSRYPGQGSPGGNRY
 ppqggggwgqphgggwgqphgggwgqphgg   50-94
                gwgqphgggwgqggg
                                  95-112  THSQWNKPSKPKTNMKHM
        agaaaagavvgglggymlgsams  113-135
                                 136-187  RPIIHFGSDYEDRYYRENMHRYPNQVYYRP
                                          MDEYSNQNNFVHDCVNITIKQH
                 tvttttkgenftet  188-201
                                 202-236  DVKMMERVVEQMCITQYERESQAYYQRGSS
                                          MVLFS
               sppvillisflifliv  237-252
                                 253-253  G

The low-complexity sequences are on the left (lower case) and high-complexity sequences are on the right (upper case). All sequence segments read from left to right and their order in the sequence is from top to bottom, as shown by the central column of residue numbers.

The command line:

  ncbi-seg /usr/share/doc/ncbi-seg/examples/prion.fa -x

gives the following FASTA-formatted file:-

 >PRIO_HUMAN MAJOR PRION PROTEIN PRECURSOR
 MANLGCWMLVLFVATWSDLGLCKKRPKPGGWNTGGSRYPGQGSPGGNRYxxxxxxxxxxx
 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxTHSQWNKPSKPKTNMKHMxxxxxxxx
 xxxxxxxxxxxxxxxRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCV
 NITIKQHxxxxxxxxxxxxxxDVKMMERVVEQMCITQYERESQAYYQRGSSMVLFSxxxx
 xxxxxxxxxxxxG

AUTHORS

John Wootton: [email protected]

Scott Federhen: [email protected]

 National Center for Biotechnology Information
 Building 38A, Room 8N805
 National Library of Medicine
 National Institutes of Health
 Bethesda, Maryland, MD 20894
 U.S.A.

PRIMARY REFERENCE

Wootton, J.C., Federhen, S. (1993) Statistics of local complexity in amino acid sequences and sequence databases. Computers & Chemistry 17: 149-163.

OTHER REFERENCES

Wootton, J.C. (1994) Non-globular domains in protein sequences: automated segmentation using complexity measures. Computers & Chemistry 18: (in press).

Altschul, S.F., Boguski, M., Gish, W., Wootton, J.C. (1994) Issues in searching molecular sequence databases. Nature Genetics 6: 119-129.

Wootton, J.C. (1994) Simple sequences of protein and DNA. In: Nucleic Acid and Protein Sequence Analysis: A Practical Approach. (Second Edition, Chapter 8, Bishop, M.J. and Rawlings, C.R. Eds. IRL Press, Oxford) (In press).