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PROTEIN SEQUENCE (maximum length 2000)
A top line containining ">something" will be thrown out, if included.


We use a fast algorithm to search for repeating fragments within protein sequences. The technique is based on an extension of the Smith-Waterman algorithm that allows the calculation of sub-optimal alignments of a sequence against itself. We are able to estimate the statistical significance of all sub-optimal alignment scores. We also rapidly determine the length of the repeating fragment and the number of times it is found in a sequence.
[Source Code]
More information:
Matteo Pellegrini
This page has been accessed "; # get_count("/usr/httpd/html/DOE/Services/Repeats/.counts", "muffin", "repeats","gif"); # print " times since October 9, 2002"; print $tail; ############################################################################### Function a_good_input_sequence($ss) { $len = strlen($ss); $ret=""; for($ix=0;$ix<$len;$ix++) { $aletter = $ss[$ix]; if($aletter === "\n") continue; // skip new lines else if($aletter === " ") continue; // skip new lines else if($aletter === ' ') continue; // skip spaces else if($aletter=== '') continue; if(not_an_aminoacid($aletter)) { if($aletter) { print "
Found $aletter at position. changing to '-'"; $aletter='-'; } } $ret .= $aletter; } return strtoupper($ret); } ############################################################################### Function not_an_aminoacid($cc) { global $aa,$numAA; $ret=TRUE; for($jx=0;$jx<$numAA;$jx++) { if($cc===$aa[$jx]) { $ret=FALSE; $jx=$numAA; } } return $ret; } ############################################################################### Function remove_interior_whitespace($str) { $exstr = explode(" ", $str); $ret = ""; foreach($exstr as $anelem) { $pce = ""; $pce = trim($anelem); $ret .= $pce; } return $ret; } ############################################################################### Function remove_newlines($ss) { $searchstr = "'([\r\n]\ )[\s]+'"; # $rets = preg_replace($searchstr,"",$ss); $rets = preg_replace("/\n/","",$ss); # $rets = str_replace("\n","",$ss); return $rets; } ############################################################################### Function remove_rvcode($ss) { if($ss[0]==='>') { $rets = strstr($ss,"\n"); $rets = trim($rets); } else $rets = $ss; return $rets; }