In WERAM 1.0, we try to make it more powerful and convenient to be used. This USAGE is prepared for the online service. The WERAM 1.0 provides the browse, search and advance options.
1.Browse. Two simple ways have been provided for users to browse protein of histone acetylation or methylation in database. Users can browse by species or by family classifications. Species browse allows user to choose interested animals, fungi and plants. Family browse allows user to select interested family.
EXAMPLE: Please first click on the species phylogenetic trees or family classification picture and enter specific browse webpage. Then by selecting species or family, the related protein of histone acetylation or methylation will be presented.
2. Search. Five search options are provided, including simple search,Batch Search, advance search and BLAST search.
EXAMPLE: You can click on the "Example" button to load an instance. All species containing "KAT2A" histone acetyltransferase will be shown by clicking on the "Submit" button.
Specifically, we add a new "Substrate Example" button. You can click on the"Substrate Example" button to load an instance. All protein that can specifically recognize the "H3K27" site will be shown.
(2) Batch search. You can input one keyword to search several Proteins the WERAM 1.0. The search fields include WERAM ID, Ensembl Protein ID, Ensembl Gene ID, Ensembl Transcript ID, UniProt Accession, Gene Name/Alias and Substrate.
EXAMPLE: You can click on the "Example" button to load an instance. All species containing Ensembl Protein ID like "ENSP00000263801; ENSP00000357330; ENSP00000385442; ENSP00000446880; ENSP00000269397" will be shown by clicking on the "Submit" button. And also, you can use the "Substrate Example" button.
(3) Advance search. allows you to input up to three terms to find the information more specifically. The querying fields can be empty if less terms are needed. The three terms could be connected by the following operators:
exclude: If selected, the term following this operator must be not contained in the specified field(s)
EXAMPLE: You can click on the "Example" button to load an instance; the human protein histone methyltransferase family "SET2" will be shown by clicking on the "Submit" button.
(4) Histone Regulator Detection. This section can provide protein of histone acetylation and methylayion classification information of an unknown sequence submitted by user, including group, family, score, e-value, domain length and alignment information. If sequence can't be classified into any family, the program will tell you "No hits found". The details of classification method are available in paper.
EXAMPLE: You can click on the "Example1" or "Example2" button to load an instance, which could make a classification on given sequence. The result will be presented following by clicking on submit button.
(5) BLAST search. This option is used to find the specific protein and/or related homologues by sequence alignment. This search-option will help you to find the querying protein accurately and fast. Only one protein sequence in FASTA format is allowed per time. The E-value threshold could be user-defined, while the species information could be specified. The default parameters of E-value and species are 0.01 and H. Sapiens, respectively.
EXAMPLE: You can click on the "Example" button to load the protein sequence of human methylation reader protein. By clicking on the "Submit" button, you can find the related homologues in H. Sapiens.
Frequently Asked Questions:
1. Q: Can the search result display the protein’s function in the methylation system and acetylation system at the same time?
A: If you input a protein that has the potential to be the function actor in both two systems, we will display all the possible role it can be.
A:The protein is annotated as reviewed or unreviewed according to whether it has been reported by the paper. For example, if a protein is clearly reported that it has the specific function like transferring the methyl group, we will mark it as "Reviewed". If a protein is found by predict but without paper’s supports, we will annotate it as "Unreviewed".
3. Q: I have a few questions which are not listed above, how can I contact the authors of WERAM?
A: Please contact the three major authors: Dr. Yu Xue, Yang Xu and Shuang Zhang for details.