lalign.1

.TH LALIGN/PLALIGN 1 local
.SH NAME
lalign \- compare two protein or DNA sequences for local similarity and show the local sequence alignments

plalign,flalign \- compare two sequences for local similarity and plot the local sequence alignments

.SH SYNOPSIS
.B lalign
[-EKfgiImnNOQqrRswxZ] sequence-file-1 sequence-file-2 
.br
.B plalign
[-EKfgiImnNQqrRsvwxZ] sequence-file-1 sequence-file-2 

.SH DESCRIPTION
.B lalign
and
.B plalign
programs compare two sequences looking for local sequence
similarities.
.B lalign/plalign
use code developed by X. Huang and W. Miller (Adv. Appl. Math. (1991)
12:337-357) for the "sim" program.  (Version 2.1 uses sim2 code.) While
.B ssearch
reports only the best alignment between the query sequence and the
library sequence,
.B lalign
and
.B plalign
will report all the alignments with pair-wisse probabilities < 0.05 (default,
modified with -E #) between the two sequences
.B lalign
shows the actual local alignments between the two sequences and their
scores, while
.B plalign
produces a plot of the alignments that looks similar to a
`dot-matrix' homology plot.  On Unix\(tm systems,
.B plalign
generates postscript output.
.B flalign
generates graphic commands for the GCG "figure" program.
.PP
Probability estimates for the 
.B lalign/plalign/flalign
programs are based on the parameters provided by Altschul and Gish
(1996) Meth. Enzymol. 266:460-480.  These parameters are available for
BLOSUM50, BLOSUM62, and PAM250 scoring matrices with specific gap
penalties, and also for DNA comparison with a gap penalty of -16, -4.
Probability estimates are not available for other scoring matrices and
gap penalties.
.PP
The E(10,000) values reported with the alignments are the
pairwise-alignment probabilities multiplied by 10,000. These estimates
approximate the significance from a search of a 10,000 entry database.
They differ from the -E 0.05 initial theshold by the same factor of
10,000.  This is an unfortunate inconsistency, but I believe that
it is helpful to provide the perspective of a database search.
.PP
The
.B lalign/plalign/fasta
programs use a standard text format sequence file.  Lines beginning
with '>' or ';' are considered comments and ignored; sequences can be upper or
lower case, blanks,tabs and unrecognizable characters are ignored.
.B lalign/plalign
expect sequences to use the single letter amino acid codes, see
.B protcodes(1)
\&.
.SH OPTIONS
.PP
.B lalign
and the other programs can be directed to change the scoring matrix,
search parameters, output format, and default search directories by
entering options on the command line (preceeded by a `\-'). All of the
options should preceed the file name and ktup arguments). Alternately,
these options can be changed by setting environment variables.  The
options and environment variables are:
.TP
\-E #
Pairwise-probability limit (default -E 0.05).
.TP
\-K #
maximum number of alignments to be shown (default -K 50).
.TP
\-f #
Penalty for the first residue a gap (-14 by default).
.TP
\-g #
Penalty for each additional residue in a gap (-4 by default).
.TP
\-i
Compare the reverse complement (DNA only).
.TP
\-I
Show alignment between identical sequences.  Normally, the identity
alignment is not shown.
.TP
\-m #
.B (MARKX)
=1,2,3. Alternate display of matches and mismatches in
alignments. MARKX=1 uses ":","."," ", for identities, consevative
replacements, and non-conservative replacements, respectively. MARKX=2
uses " ","x", and "X".  MARKX=3 does not show the second sequence, but
uses the second alignment line to display matches with a "."  for
identity, or with the mismatched residue for mismatches.  MARKX=3 is
useful for aligning large numbers of similar sequences.
.TP
\-n
pre-specify DNA sequence, rather than infer from  sequence.
.TP
\-N #
limit first and second sequences to '#' residues.
.TP
\-s str
.B (SMATRIX)
the filename of an alternative scoring matrix file.  For protein
sequences, BLOSUM50 is used by default; PAM250 can be used with the
command line option
.B -s P250\c
\&, BLOSUM62 with "-s BL62".
.TP
\-v str
.B (LINEVAL)
(plalign only)
.B plalign
can use up to 4 different line styles to denote the
scores of local alignments.  The scores that correspond to these
line styles can be specified with the environment variable
.B LINVAL\c
\&, or with the
.B \-v
option.  In either case, a string with three numbers separated by
spaces should be given.  This string must be surrounded by double
quotation marks.  For example, LINEVAL="200 100 50" tells plalign
to use solid lines for local alignments with scores greater than 200,
long dashed lines for scores between 100 and 200, short dashed lines
for scores between 50 and 100, and dotted lines for scores less than 50.
.in +0.5i
plalign -v "200 100 50"
.in -0.5i
Normally, the values are 200, 100, and 50 for protein sequence comparisons
and 400, 200, and 100 for DNA sequence comparisons.
.TP
\-w #
.B (LINLEN)
output line length for sequence alignments.  (normally 60,
can be set up to 200).
.SH EXAMPLES
.TP
(1)
.B lalign
mchu.aa mchu.aa
.PP
Compare the amino acid sequence in the file mchu.aa with itself and
report the ten best local alignments.  Sequence files should have the form:
.nf
.in +5n

>MCHU - Calmodulin - Human ...
ADQLTEEQIAEF ...
.in +0n

.fi
.TP
(2)
.B plalign
-K 100 -E 0.01 qrhuld.aa egmsmg.aa 
.PP
Display up to 100 local alignments of the LDL
receptor (qrhuld.aa) with epidermal growth factor precursor
(egmsmg.aa) with pairwise probabilities better than 0.01.
Plot the results on the screen.
.TP
(3)
.B lalign
.PP
Run the
.B lalign
program in interactive mode.  The program will prompt for
the name of two sequence files and the number of alignments to show.
.SH "SEE ALSO"
ssearch(1), prss(1), fasta(1), protcodes(5), dnacodes(5)
.SH AUTHOR
Bill Pearson
.br
wrp@virginia.EDU