PROF_PAT: Getting Started

PROF_PAT is a collection of patterns constructed for protein families.

For your protein sequences, you can search these sequences against PROF_PAT. This search will tell you if they have matched any of the patterns in PROF_PAT and if so, you will automatically be told how many motifs of each pattern are matched, where they lie in the sequence.

To do this you should get your sequences in FASTA format:

>NAME of the first sequence
SEQUENCE
>NAME of the second sequence
.....

Having got your sequences you are going to need to cut and paste them into search form.

You can take the sequences from a file using option 'From File'.

You should specify (or agree default values): the lower level of similarity (see INFO), select a scoring matrix for amino acid residues, and a number of the best matchings to display.

Then hit 'Search PROF_PAT' and wait for some seconds depending on the load on the server. You should get back a page looking like

Parameters: =2, =80, =250PAM, =2
>NAME of the first sequence
 SEQUENCE
ID 12008(18) - Score=161.48 (family) 
DE YDL147W
DE PROTEASOME SUBUNIT P55
DE CEMSE45F
    4   49 
    5   84 
    6   95 
    7  119 
    8  136 
    9  146 
   10  158 
   11  169 
   12  195 
   13  222 
   14  256 
   15  268 
   16  281 
   17  312 
   18  351 
ID 10891(57) - Score=19.625 (family)
DE CHROMOSOME SEGREGATION PROTEIN CUT3
DE CHROMOSOME ASSEMBLY PROTEIN XCAP-C
   15   22 
   20   67 
   39  104 
   45  205 
   46  339
>NAME of the second sequence
.....