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

SYNOPSIS

lalign [-EKfgiImnNOQqrRswxZ] sequence-file-1 sequence-file-2
plalign [-EKfgiImnNQqrRsvwxZ] sequence-file-1 sequence-file-2

DESCRIPTION

lalign and plalign programs compare two sequences looking for local sequence similarities. 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 ssearch reports only the best alignment between the query sequence and the library sequence, lalign and plalign will report all the alignments with pair-wisse probabilities < 0.05 (default, modified with -E #) between the two sequences lalign shows the actual local alignments between the two sequences and their scores, while plalign produces a plot of the alignments that looks similar to a `dot-matrix' homology plot. On Unix™ systems, plalign generates postscript output. flalign generates graphic commands for the GCG "figure" program.

Probability estimates for the 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.

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.

The 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. lalign/plalign expect sequences to use the single letter amino acid codes, see protcodes(1) .

OPTIONS

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:

-E #: Pairwise-probability limit (default -E 0.05).
-K #: maximum number of alignments to be shown (default -K 50).
-f #: Penalty for the first residue a gap (-14 by default).
-g #: Penalty for each additional residue in a gap (-4 by default).
-i: Compare the reverse complement (DNA only).
-I: Show alignment between identical sequences. Normally, the identity alignment is not shown.
-m #: (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.
-n: pre-specify DNA sequence, rather than infer from sequence.
-N #: limit first and second sequences to '#' residues.
-s str: (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 -s P250, BLOSUM62 with "-s BL62".
-v str: (LINEVAL) (plalign only) 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 LINVAL, or with the -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.
plalign -v "200 100 50"
Normally, the values are 200, 100, and 50 for protein sequence comparisons and 400, 200, and 100 for DNA sequence comparisons.
-w #: (LINLEN) output line length for sequence alignments. (normally 60, can be set up to 200).

EXAMPLES

(1): lalign mchu.aa mchu.aa

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:



>MCHU - Calmodulin - Human ...
ADQLTEEQIAEF ...

(2): plalign -K 100 -E 0.01 qrhuld.aa egmsmg.aa

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.

(3): lalign

Run the lalign program in interactive mode. The program will prompt for the name of two sequence files and the number of alignments to show.

AUTHOR