--- /dev/null
+
+DOCUMENTATION OF SEG (FROM 'MAN' PAGE)
+--------------------------------------
+
+
+NAME
+----
+ seg - segment sequence(s) by local complexity
+
+
+SYNOPSIS
+--------
+ seg sequence [ W ] [ K(1) ] [ K(2) ] [ -x ] [ options ]
+
+
+DESCRIPTION
+-----------
+
+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. 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 'seg sequence' (equivalent to '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:
+
+ seg database 12 1.8 2.0 -x
+
+Homopolymer analysis:
+--------------------
+To examine all homopolymeric subsequences of length (for example)
+7 or greater:
+
+ seg sequence 7 0 0
+
+Non-globular regions of protein sequences:
+-----------------------------------------
+Many long non-globular domains may be diagnosed at longer window
+lengths, typically:
+
+ seg sequence 45 3.4 3.75
+
+For some shorter non-globular domains, the following set is
+appropriate:
+
+ 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:
+
+ 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:
+
+ seg prion
+
+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:
+
+ seg prion -x
+
+gives the following FASTA-formatted file:-
+
+>PRIO_HUMAN MAJOR PRION PROTEIN PRECURSOR
+MANLGCWMLVLFVATWSDLGLCKKRPKPGGWNTGGSRYPGQGSPGGNRYxxxxxxxxxxx
+xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxTHSQWNKPSKPKTNMKHMxxxxxxxx
+xxxxxxxxxxxxxxxRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCV
+NITIKQHxxxxxxxxxxxxxxDVKMMERVVEQMCITQYERESQAYYQRGSSMVLFSxxxx
+xxxxxxxxxxxxG
+
+
+
+SEE ALSO
+--------
+
+segn, blast, saps, xnu
+
+
+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).
+
+
git://source.jalview.org / jpred.git / blobdiff