| Program | Description |
| FASTA |
Compares a protein sequence to another protein sequence or to a protein
database, or a DNA sequence to another DNA sequence or a DNA library.
|
|
SSEARCH |
Perform a rigorous Smith-Waterman alignment between a protein
sequence and another protein sequence or a protein database.
|
|
GGSEARCH/ GLSEARCH |
Perform a rigorous Global/Global (GGSEARCH) or Global/Local (GLSEARCH)
alignment between a protein sequence and another protein sequence or a
protein database. GGSEARCH implements a
Needleman-Wunsch like alignment, except that affine gap penalties are
used. GLSEARCH is
most appropriate for global searches with a domain, which require local
alignments within proteins.
|
FASTX/
FASTY |
Compares a DNA sequence to a protein sequence database, translating
the DNA sequence in three forward (or reverse) frames and allowing
frameshifts.
|
PRSS/
PRFX
|
Evaluates the significance of pairwise similarity scores using a Monte
Carlo analysis. The Smith-Waterman local similarity score for the two
sequences is calculated, and then the statistical parameters Lambda
and K from the random scores calculated by aligning the first sequence to 200 to 1000 times shuffles of the second sequence. PRFX
does a similar shuffle, but compares a translated DNA sequence to a
protein sequence using the FASTX algorithm.
PRSS/PRFX can either shuffle the second sequence in its entirety
(uniform shuffling) or shuffle the second sequence in 20 residue
segments (window shuffle). This latter strategy preserves local amino
acid composition biases, e.g. in transmembrane segments.
|
TFASTX/
TFASTY
|
Compares a protein sequence to a DNA sequence or DNA sequence
library. The DNA sequence is translated in three forward and three reverse
frames, and the protein query sequence is compared to each of the six derived
protein sequences. The DNA sequence is translated from one end to
the other; no attempt is made to edit out intervening sequences.
|
FASTS/
TFASTS
|
Compares set of short peptide fragments, as would be obtained
from mass-spec. analysis of a protein, against a
protein (fasts) or DNA (tfasts) database. A
different format is required to specify the ordered peptide mixture:
>mgstm1
MILG,MLLEYTD,MGDAP
indicates three peptide fragments were found: MILG,
MLLEYTD, and MGDAP. The commas (,) are
required to indicate the number of fragments in the mixture, but there
should be no comma after the last residue.
|
LALIGN/
PLALIGN |
Compares two protein sequences to identify regions of internal sequence
similarity. While FASTA reports a single alignment between
two sequences, LALIGN will report several sequence alignments if there
are several similar regions. LALIGN reports sequence alignments and
similarity scores. PLALIGN plots out a graph of the sequence alignments,
which looks much like a "dot-plot".
|
|
GREASE
|
Kyte-Doolittle hydropathy plot. A modern transmembrane prediction program
is available from tmpred |
GARNIER/
CHOFAS
|
Protein secondary structure prediction (provided for teaching purposes
only). Much better prediction algorithms are available from psipred
and PredictProtein
|