Provided by: ncbi-seg_0.0.20000620-1_amd64 
NAME
ncbi-seg - segment sequence(s) by local complexity
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
SEE ALSO
segn(1), blast(1), saps(1), xnu(1)
AUTHORS
John Wootton: wootton@ncbi.nlm.nih.gov
Scott Federhen: federhen@ncbi.nlm.nih.gov
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).