This seems to
be rather significant. Let us consider the example as derived
above and compute the probability of two options:
sequence fragment 1: GDRD
sequence fragment 2: GERL
option 1: pattern description: G(D,E)R(D,L)
option 2: pattern description: G(D,E)X(D,L)
The probability of option 1 is calculated with changed
values at position 2 and 4 as we have two alternatives each:
1 1 1 1
---- * ---- * ---- * ---- = 0.000025 = 0.0025 %
20 10 20 10
The probability of option 2 has a "joker" in position
3, and as we will not find sequences less than four residues
in sequence databases we can set the probability to find an X
in a tetra-peptide at position three as 1:
1 1 1
---- * ---- * 1 * ---- = 0.0005 = 0.05 %
20 10 10
The value of less than a promille looks low, but is much
too high in order to allow a very sensitive searching. Assume
a database of 50000 sequences and further that a match can occur
only once. (This is a crude guess as the chance of pattern occurrence
depends on the composition). By chance, we would have 0.0005
multiplied by 50000 which results in 25 hits - by random chance!
Programs
The 'findpatterns' Program
findpatterns
searches
databases (e.g., genembl:*),
a file of sequence names (e.g., @my.fil, or my.msf{*}, see later ), or
single sequences (e.g., my.seq) for patterns. The patterns are
reported with exact matches, as shown below. If databases are
searched, the nomonitor option is recommended.
Databases available at Basel
University include:
Database name GCG name contents
----------------------------------------------------------------
EMBL + Updates
GENBANK + Updates
(GB as exclusion set) GENEMBL: all DNA databases (1)
SWISSPROT SWISSPROT: most proteins (2)
PIR International PIR: most proteins
PATCHX + PIR MIPSX: MIPS merged database (3)
NEW entries of EMBL XEMBL: EMBL new entries (4)
UPDATED entries EMBL XXEMBL: EMBL updated entries (5)
GENBANK update excl. GB_NEW: GENBANK exclusion (6)
1) The definition of GENEMBL can vary. Depending on the
location, you can use either GENBANK with an exclusion set of
EMBL data not found in GENBANK, or vice versa (e.g., in Basel).
Depending on whether you are connected to a network which is
used to update data on a periodic basis, the GENEMBL set may
include also daily updates.
2) containing weekly updates
3) PATCHX is updated quarterly and includes the previous release
of SWISSPROT, an automatic translation of EMBL, and some other
databases.
4) The definitions vary. XEMBL, EM_NEW, EMBL_DAILY, GB_NEW, XSWISS,
SW_NEW, PIR4, etc. are names that denote the character of the
preliminary entries.
5) This is a Basel-specific item. The main purpose of this database
is to find new data in the annotation, as updates rarely include
changes in the sequence. In order to have the main EMBL database
show not too many entries in FASTA runs, the XXEMBL database
is not included in the usual GENEMBL set.
6) This is a Basel-specific item. The weekly updated GENBANK
database is calculated against EMBL and XEMBL to find those entries
which are not in the EMBL updates yet. Additional databases are
available at Basel. Their names are displayed when you start
the molecular biology environment. Examples are Amos Bairoch's
PROSITE database of protein motifs, or Rich Robert's REBASE database
of restriction enzymes.
NOTE: The term GENEMBLPLUS, introduced in GCG version 8.1, is
equivalent to GENEMBL. This is a deviation from the standard
GCG installation which uses GENEMBL:* to describe all databases
except EST and STS sections.
$ findpatterns/nomon
FINDPATTERNS identifies sequences with short pattern queries like
GAATTC or YRYRYRYR. You can define the patterns ambiguously and
allow mismatches. You can provide the patterns in a file or simply
type them in from the terminal.
FINDPATTERNS in what sequence(s) ? genembl:*
Enter patterns individually, one per line. End the list with a blank line.
Pattern 1: G(D,E)(X){0,2}R(D,L)
Pattern 2:
What should I call the output file (* FindPatterns.Find *) ? <RETURN>
JAMF source code
BioCompanion V2.x (1995)