Provided by: sim4_0.0.20121010-5_amd64 
NAME
sim4 - align an expressed DNA sequence with a genomic sequence
SYNOPSIS
sim4 seqfile1 seqfile2 {[WXKCRDAPNB]=value}
DESCRIPTION
sim4 is a similarity-based tool for aligning an expressed DNA sequence (EST, cDNA, mRNA) with a genomic
sequence for the gene. It also detects end matches when the two input sequences overlap at one end (i.e.,
the start of one sequence overlaps the end of the other). If seqfile2 is a database of sequences, the
sequence in seqfile1 will be aligned with each of the sequences in seqfile2.
sim4 employs a blast-based technique to first determine the basic matching blocks representing the "exon
cores". In this first stage, it detects all possible exact matches of W-mers (i.e., DNA words of size W)
between the two sequences and extends them to maximal scoring gap-free segments. In the second stage, the
exon cores are extended into the adjacent as-yet-unmatched fragments using greedy alignment algorithms,
and heuristics are used to favor configurations that conform to the splice-site recognition signals (GT-
AG, CT-AC). If necessary, the process is repeated with less stringent parameters on the unmatched
fragments.
By default, sim4 searches both strands and reports the best match, measured by the number of matching
nucleotides found in the alignment. The R command line option can be used to restrict the search to one
orientation (strand) only.
Currently, five major alignment display options are supported, controlled by the A option. By default
(A=0), only the endpoints, overall similarity, and orientation of the introns are reported. An arrow sign
(`->' or `<-') indicates the orientation of the intron (`+' or `-' strand), when the signals flanking the
intron have three or more position matches with either the GT-AG or the CT-AC splice recognition signals.
When the same number of matches is found for both orientations, the intron is reported as ambiguous, and
represented by `--'. The sign `==' marks the absence from the alignment of a cDNA fragment starting at
that position. Alternative formats (lav-block format, text, PipMaker-type `exons file', or certain
combinations of these options) can be requested by specifying a different value for A.
If the P option is specified with a non-zero value, sim4 will remove any 3'-end poly-A tails that it
detects in the alignment.
Occasionally, sim4 may miss an internal exon when surrounded by very large introns, typically longer than
100 Kb. When this is suspected, the H option can be used to reset the exons' weight to compensate for the
intron gap penalty.
Ambiguity codes are by default allowed in sequence data, but sim4 treats them non-differentially. If
desired, the B command option can restrict the set of acceptable characters to A,C,G,T,N and X only.
sim4 compares the lengths of the input sequences to distinguish between the cDNA (`short') and the
genomic (`long') components in the comparison. When seqfile2 contains a collection of sequences, the
first entry in the file will be used to determine the type of this and all subsequent comparisons.
In the description below, the term MSP denotes a Maximal Segment Pair, that is, a pair of highly similar
fragments in the two sequences, obtained during the blast-like procedure by extending a W-mer hit by
matches and perhaps a few mismatches.
OPTIONS
The algorithm parameters (included in the first two sections below) have already been tuned and do not
normally require adjustment by the user.
Parameters internal to the blast-like procedure:
W Sets the word size for blast hits in the first stage of the algorithm. The default value is 12,
but it can be increased for a more stringent search or decreased to find weaker matches.
X Controls the limits for terminating word extensions in the blast-like stage of the algorithm. The
default value is 12.
K Sets the threshold for the MSP scores when determining the basic `exon cores', during the first
stage of the algorithm. (If this option is not specified, the threshold is computed from the
lengths of the sequences, using statistical criteria.) For example, a good value for genomic
sequences in the range of a few hundred Kb is 16. To avoid spurious matches, however, a larger
value may be needed for longer sequences.
C Sets the threshold for the MSP scores when aligning the as-yet-unmatched fragments, during the
second stage of the algorithm. By default, the smaller of the constant 12 and a statistics-based
threshold is chosen.
Additional algorithm parameters:
D Sets the bound for the "diagonal" distance within consecutive MSPs in an exon. The default value
is 10.
Context parameters:
R Specifies the direction of the search. If R=0, only the "+" (direct) strand is searched. If R=1,
only the "-" (reverse complement) matches are sought. By default (R=2), sim4 searches both strands
and reports the best match, measured by the number of matching pairs in the alignment.
A Specifies the format of the output: exon endpoints only (A=0), exon endpoints and boundaries of
the coding region (CDS) in the genomic sequence, when specified for the input mRNA (A=5),
alignment text (A=1), alignment in lav-block format (A=2), or both exon endpoints and alignment
text (A=3 or A=4). If a reverse complement match is found, A=0,1,2,3,5 will give its position in
the "+" strand of the longer sequence and the "-" strand of the shorter sequence. A=4 will give
its position in the "+" strand of the first sequence (seqfile1) and the "-" strand of the second
sequence (seqfile2), regardless of which sequence is longer. The A=5 option can be used with the S
command line option to specify the endpoints of the CDS in the mRNA, and produces output in the
`exons file' format required by PipMaker.
P Specifies whether or not the program should report the fragment of the alignment containing the
poly-A tail (if found). By default (P=0) the alignment is displayed as computed, but specifying a
non-zero value will request sim4 to remove the poly-A tails. When this feature is enabled, all
display options produce additional lav alignment headers.
H Resets the MSPs' weight to compensate for very large introns. The default value is H=500, but some
introns larger than 100 Kb may require higher values, typically between 1000 and 2500. This option
should be used cautiously, generally in cases where an unmatched internal portion of the cDNA may
disguise a missed exon within a very large intron. It is not recommended for ESTs, where they may
produce spurious exons.
N Requests an additional search for small marginal exons (N=1) guided by the splice-site recognition
signals. This option can be used when a high accuracy match is expected. The default value is N=0,
specifying no additional search.
B Controls the set of characters allowed in the input sequences. By default (B=1), ambiguity
characters (ABCDGHKMNRSTVWXY) are allowed. By specifying B=0, the set of acceptable characters is
restricted to A,C,G,T,N and X only.
S Allows the user to specify the endpoints of the CDS in the input mRNA, with the syntax: S=n1..n2.
This option is only available with the A=5 flag, which produces output in the format required by
PipMaker. Alternatively, the CDS coordinates could appear in a construct CDS=n1..n2 in the FastA
header of the mRNA sequence. When the second file is an mRNA database, the command line
specification for the CDS will apply to the first sequence in the file only.
EXAMPLES
sim4 est genomic
sim4 genomic estdb
sim4 est genomic A=1 P=1
sim4 est1 est2 R=1
sim4 mRNA genomic A=5 S=123..1020
sim4 mouse_cDNA human_genomic K=15 C=11 A=3 W=10
AUTHORS
sim4 was written by Liliana Florea <florea@gwu.edu> and Scott Schwartz.
This manual page was written by Nelson A. de Oliveira <naoliv@gmail.com>, based on the online
documentation at http://globin.cse.psu.edu/html/docs/sim4.html, for the Debian project (but may be used
by others).
Wed, 03 Aug 2005 18:40:58 -0300 SIM4(1)