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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1"/><title></title><link rel="shortcut icon" href="favicon.ico" type="image/x-icon"/><link rel="stylesheet" type="text/css" href=".css"/></head><body><h4><a name="discepancy">Discrepancy</a></h4>Geometric discrepancy is a measure of how similar RNA structures are. Highergeometric discrepancy corresponds to more dissimilar structures. Identical structureshave discrepancy zero. Searches with high geometric discrepancy cutoffs takesignificantly longer than those with lower cutoffs.<hr><h4><a name="email">Email</a></h4>You can optionally specify your email to receive a notification once your search has completed.<hr><h4><a name="dist">Distance constraint</a></h4>Set limits on the difference between nucleotide numbers using the boxes below the diagonal.(Actually, what is used is the difference between the index of nucleotides in the file, not NDB nucleotide number.)<ul><li>To put an upper limit on the difference, type something like <5 or <=5. </li><li>To put a lower limit on the difference, type something like >5 or >=5. </li><li>To put both limits at once, type something like >5 <=12. </li><li> To insist that the nucleotide in the given row have a lower nucleotide number than the nucleotide in the given column,type <, separated by a space from other specifications. For greater, type >. </li></ul><hr><h4><a name="inter">Interactions constraints</a></h4>Basepair, base stacking, base phosphate, or letter pair constraint is specified above the diagonal.<br>To specify that all candidate motifs must have a tWH basepair between the nucleotides correspondingto the first and second nucleotides in the query motif, type tWH in the first row, second column.This means that the nucleotide in the first row must use its Watson-Crick edge,and the nucleotide in the second column must use its Hoogsteen edge.<br><br>Valid basepair specifications are <b>cWW, tWW, cWH, cHW, tWH, tHW, cWS, cSW, tWS, tSW, cHH, tHH, cHS, cSH, tHS, tSH, cSS, tSS</b>.<br> Note, however, that the cSS and tSS interactions are not, in fact, symmetric, because each base can use the sugar edge differently. Follwing Leontis, Stombaugh, Westhof (NAR 2002), type cSs to specify that the first base has priority, csS for the second, or cSS for either.<br>Specifying multiple interactions allows more ways a candidate can satisfy the constraints; for example, typing cWH cHW requires a cis Watson-Crick/Hoogsteen basepair, but either base can use the Watson-Crick edge, and the other uses the Hoogsteen edge.<br><br>The abbreviation <b>"trans"</b> gives all trans categories, <b>"cis"</b> for cis. <br>Type <b>"bif"</b> for bifurcated basepairs (see LSW 2002). <br>Type <b>~cWW</b> to exclude candidates having a cWW basepair.<br><br>Some pairs of bases are close to, say, cWW, but do not meet the strict criteria for membership in the cWW classification. Type <b>ncWW ("near cWW")</b> to get basepairs that are not classified into any category, but for which the cWW category is the closest match, up to a certain fairly generous limit. Type "cWW ncWW" to get cWW and near cWW pairs, cWW. Type ntrans to get all pairs nearest to a trans pair.<br><br>Type s35 for stacking in which the first base uses its 3 face, and the second base uses its 5 face. Similarly, type <b>s53, s33, or s55</b>. Type <b>"stack"</b> to allow all stacking interactions. The prefixes "n" and "~" work with stacking, as above.<br><br>To specify that the nucleotides must match a certain pattern, type, for example, <b>"cWW CG GC"</b> to get only CG or GC cWW pairs.<br><br>To require that two nucleotides make a base-phosphate interaction, enter <b>BPh</b> in the corresponding yellow box. This will select pairs of nucleotides in which the first nucleotide's base is a hydrogen bond donor and the second nucleotide's phosphate is an acceptor. To reverse the roles, type PhB. To specify particular base-phosphate categories, type 0BPh, 1BPh, 2BPh, ..., 9BPh, or 0PhB, 1PhB, etc. For near base-phosphate interactions, type nBPh, nPhB, n1BPh, n1PhB, etc.<br><br>One can restrict to pairs that play a certain role in the secondary and tertiary structure. For pairs that are nested, type "N" or <b>"nested"</b>. For pairs that cross nested interactions but involve nucleotides in the same branch of the RNA, type <b>"local"</b> or "L". For long-range or distant interactions, between different branches of the RNA, type <b>"long-range"</b>, "distant", "D", or "LR". Note that "nested", "local", and "distant" are mutually exclusive. They can be negated with ~, but ~local only returns distant interactions, not nested ones.<br><br>
To find bases which are in the same plane and are close enough that they
may hydrogen bond in some way, type <b>"coplanar"</b> or <b>"cp"</b>. Near and not
coplanar can be obtained with the "n" and "~" prefixes, respectively.
<br><br>
To specify bases that participate in cWW pairs and that delimit a
single-stranded region such as a hairpin loop or one strand in an
internal or junction loop, type <b>"flankss"</b> or <b>"flank"</b> or <b>"F"</b>. Note: for
internal and junction loops, flanking nucleotides will be on the same
strand, one on each side of the loop. Such flanking nucleotides usually
do not interact with one another. In a hairpin, however, the
nucleotides in the closing basepair simultaneously make a cWW pair and
satisfy the flankss relation.
<br>
<h4><a name="diagonal">Nucleotide identity constraint</a></h4>The user can impose a nucleotide identify constraint(nucleotide mask) for their search by putting in nucleotide constraintsin the text-boxes on the diagonal in the Interaction Matrix, which has a white background. <br>Typing 'A', for instance, means that only candidate motifswith an A in the corresponding position will be kept.Typing 'AG' allows either A or G, etc.<br>The program uses these standard abbreviations for other combinations:<br>M for A or C<br>R for A or G<br>W for A or U<br>S for C or G<br>Y for C or U<br>K for G or U<br>V for A, C, or G<br>H for A, C, or U<br>D for A, G, or U<br>B for C, G, or U<br>N for A, C, G, or U<br><br>Note that N is the default. One may also exclude a given base using the syntax '~G'for instance, to exclude candidates with a G in the corresponding position.<hr><h4><a name="ntsinput">Nucleotide numbers</a></h4>Nucleotides must be separated by commas, you can specify ranges using colons.You can insert any number of spaces. The ordering of nucleotides doesn't matter.<br>These examples are equivalent:<br>1856:1860, 1882:1886<br>1860:1856, 1886:1882<br>1856,1857:1859,1860,1882:1884,1885,1886<br>1856,1857,1858,1859,1860,1882,1883,1884,1885,1886<br><hr><h4><a name="where">RNA-containing PDB files</a></h4>The list of PDB files is regularly updated to include all available RNA-containing PDB files.If you do not see a file, please let us know about it using the contact form.<br>It also includes several non-redundant list of PDB files at various resolutions. More information aboutthe non-redundant lists can be found <a href='http://rna.bgsu.edu/fr3d/AnalyzedStructures/Nonredundant_All_Resolution.html'>here</a> and <a href='http://nar.oxfordjournals.org/content/37/7/2294.abstract'>here</a>. In the next updates of WebFR3D, these lists will be automatically updated on a weekly basis. <br><br></body></html>