plalign - compare two sequences for local similarity and plot the local
lalign [-fgOmsw] sequence-file-1 sequence-file-2 [ #-of-alignments ]
plalign [-fgmsv] sequence-file-1 sequence-file-2 [ #-of-alignments ]
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" pro-
gram. While ssearch reports only the best alignment between the query
sequence and the library sequence, lalign and plalign will report a
specified number of alignments (the default is 10) between the two
sequences lalign shows the actual local alignments between the two
sequences and their scores, while plalign produces a plot of the align-
ments that looks similar to a 'dot-matrix' homology plot. On Unix(TM)
systems, plalign generates postscript output.
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 unrecog-
nizable 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 directo-
ries by entering options on the command line (preceeded by a '-'). All
of the options should preceed the file name and ktup arguments). Alter-
nately, 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, conseva-
tive replacements, and non-conservative replacements, respec-
tively. MARKX=2 uses " ","x", and "X". MARKX=3 does not show
the second sequence, but uses the second alignment line to dis-
play 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
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
>MCHU - Calmodulin - Human ...
(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.
Run the lalign program in interactive mode. The program will prompt
for the name of two sequence files and the number of alignments to
ssearch(1), rss(1), fasta(1), protcodes(5), dnacodes(5)