plalign - compare two sequences for local similarity and plot the local sequence alignments
plalign [-fgmsv] sequence-file-1 sequence-file-2 [ #-of-alignments ]
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) .
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:
-f # Penalty for the first residue a gap (-14 by default).
-g # Penalty for each additional residue in a gap (-4 by default).
-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.
-s str
(SMATRIX) the filename of an alternative scoring matrix file. For
protein sequences, PAM250 is used by default; PAM120 can be used with
the command line option -s 120.
-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).
(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 qrhuld.aa egmsmg.aa 50
Display the 50 best local alignments of the LDL receptor (qrhuld.aa) with epidermal growth factor precursor (egmsmg.aa). 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.