genesbymotifsearch: Find genes whose protein product contains a motif pattern...
In duncantl/REuPathDB: Interface to REST API of (EuPathDB)

Description Arguments Value

Find genes whose protein product contains a motif pattern that you specify., e.g. "CC6+RK", which means "two cysteines followed by one or more hydrophobic amino acids, followed by arginine, then lysine". The pattern need not be well conserved. If you can describe it in words, you can probably use this tool to create an "expression" that can search other proteins for similar patterns.

Another example is the pattern of the <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15591202&query_hl=2"> Pexel motif</a>, which can be represented as "R.L.[EQD]", meaning "an arginine, then any amino acid, then a leucine, then any amino acid, then either an aspartic acid, a glutamic acid, or a glutamine".

The pattern need not be well conserved. If you can describe it in words, you can probably use this tool to create an "expression" that can search other proteins for similar patterns.

Specify the pattern with a (Perl style) "regular expression". (Regular expressions are more powerful than PROSITE patterns.) For a description of how to create regular expressions, please see the <a href="regexp.jsp">Regular Expression Tutorial</a>.

The following codes can be used to represent classes of amino acids. <table border columns=3> <TR> <TD>AA property </TD> <TD>Amino acids </TD> <TD>Code </TD> </TR>

<TR> <TD> Acidic </TD> <TD>DE </TD> <TD>0 </TD> </TR> <TR> <TD>Alcohol </TD> <TD>ST </TD> <TD>1 </TD> </TR> <TR> <TD>Aliphatic </TD> <TD>ILV </TD> <TD>2 </TD> </TR> <TR> <TD>Aromatic </TD> <TD>FHWY </TD> <TD>3 </TD> </TR> <TR> <TD>Basic </TD> <TD>KRH </TD> <TD>4 </TD> </TR> <TR> <TD>Charged </TD> <TD>DEHKR </TD> <TD>5 </TD> </TR> <TR> <TD>Hydrophobic </TD> <TD>AVILMFYW </TD> <TD>6 </TD> </TR> <TR> <TD>Hydrophilic </TD> <TD>KRHDENQ </TD> <TD>7 </TD> </TR> <TR> <TD>Polar </TD> <TD>CDEHKNQRST </TD> <TD>8 </TD> </TR> <TR> <TD>Small </TD> <TD>ACDGNPSTV </TD> <TD>9 </TD> </TR> <TR> <TD>Tiny </TD> <TD>AGS </TD> <TD>B </TD> </TR> <TR> <TD>Turnlike </TD> <TD>ACDEGHKNQRST </TD> <TD>Z </TD> </TR> <TR> <TD>Any </TD> <TD>ACDEFGHIKLM NPQRSTVWY </TD> <TD>. </TD> </TR> </table>

`motif_organism`	Choose one or more organisms to search with the given motif Provide one or more values. Use comma as a delimter.
`motif_expression`	Enter a Perl regular expression describing the desired motif. Example: 'CC6+RK' searches for two consecutive cysteine residues followed by a stretch of hydrophobic amino acids followed by the aminoacids arginine and lysine.
`o-fields`	Single valued attributes of the feature. Provide one or more values. Use comma as a delimter.
`o-tables`	Multi-valued attributes of the feature. Provide one or more values. Use comma as a delimter.
`.convert`	a logical value or a function that controls how the result of the method is returned. If this is a function, the character string or raw vector is passed to this function and it converts it appropriately. If this is a logical value and `TRUE`, then we attempt to convert the result based on its Content-Type returned by the Web server. If this is `FALSE`, the value from the Web server is returned as is.
`.url`	the URL for the Web request. This defaults to the correct value, but can be specified by the caller if the method is available at a different URL, e.g. locally or in a mirror server.
`.json`	a logical value controlling whether to use the JSON or the XML version of the method