PROFILEMAKE creates a symbol comparison file based on a group of aligned sequences, ie: the "profile" of the aligned sequences.
$ Profilemake/stringent
PROFILEMAKE of what aligned sequences ? chn.msf{*}
chn.msf{Avms67}, begin: 1 end: 145 len: 145 weight:
1.00
chn.msf{Evrtr2}, begin: 1 end: 145 len: 145 weight:
1.00
chn.msf{Hvcqg4}, begin: 1 end: 145 len: 145 weight:
1.00
What should I Call the output profile (* Chn.Prf *) ?
PROFILEGAP shows a BESTFIT-like alignment of a sequence to a profile. Using /GLObal performs a GAP alignment, ie: across the whole sequence:
$ Profilegap/global
(Global) PROFILEGAP of what sequence(s) ? pir1:avms67
Begin (* 1 *) ?
End (* 144 *) ?
and what profile (* Avms67.Prf *) ? chn.prf
What is the gap weight (* 4.50 *) ?
What is the gap length weight (* 0.05 *) ?
What should I Call the paired output display file (* Chn.Pair *) ?
Type the CHN.PAIR file to see the alignment between the sequence and the profile which was calculated using PIR1:AVMS67 and similar sequences. As with GAP you may get a different alignment for different gap weightings. Also examine the comparison to PIR1:AVMST5.
As with GAP you may get a different alignment for different gap weightings.
PROFILESEARCH is the closest we can get to a PROSRCH on the VAX. It performs a "best local homology" on all entries in a database, using the profile, and sorts out the best alignments.
$ Profilesearch
PROFILESEARCH with what query profile ? chn.prf
Search for query in what sequences(s) (* SwissProt:* *) ?
What is the gap weight (* 4.50 *) ?
What is the gap length weight (* 0.05 *) ?
What should I Call the output file (* Chn.Pfs *) ?
Submit to which batch queue (* OFFPEAK *) ?
The Z statistic is obtained after normalising all the scores against sequence length. An equation is calculated, all very similar sequences eliminated, then the equation calculated again. As with PROSRCH this gives a comparison of the alignments values for dissimilar sequences against similar sequences.
The Z score is the Standard Deviation for the derived fit.
PROFILESEGMENTS displays the best alignment of the profile to each of the sequences identified by PROFILESEARCH.
$ Profilesegments
(Local) PROFILESEGMENTS from what PROFILESEARCH output file? chn.pfs
Stop after how many alignments (* 15 *) ?
What should I call the paired output display file ( * chn.pairs *) ?
Type the CHN.PAIRS file. The sequences are scored for an optimal alignment. Note the QUALITY scores. Unlike PROSRCH only the best fit of the profile to any sequence will be found. Alternative alignments may exist.
PROFILESCAN compares a sequence to known profiles for their similarity.
$ Profilescan
PROFILESCAN of what sequence(s) ? pir1:avms67
.
.
What
profile library (* ProfileScan.fil *) ?
What should I call the paired output file (* avms67.scan *)?
What should I call the summary output file (* avms67.sum *)?
Avms67.sum shows which profiles the sequence has been checked against. Avms67.scan summarises the scores, showing any BESTFIT-like alignments to the profile.