※ USAGE

In PLMD database, we tried to make it powerful and convenient to be used. The online service and local packages were provided. This USAGE is prepared for the online service. For usage of local packages, please download the Manual. The PLMD 3.0 provide the search option and advance options.

1. Substrate Search. You can input one or multiple keywords (separated by space character) to search the PLMD database. The search fields including PLMD ID, UniProt Accession, Protein Name, Protein Alias, Gene Name, Gene Alias, Species, and Function.

EXAMPLE: Please click on the "Example" button to search "p53" in Gene Name field. By clicking on the "Submit" button, the related proteins will be shown.

2. Browse. Two simple ways have been provided for users to browse lysine modified protein in the database. Users can browse by species or by modification type. Type browse allows user to select interested type. Species browse allows user to choose interested species.

3. Advanced Options. Three advance options are provided, including advance search, browse, BLAST search.

(1) Advanced search allows you to input up to two terms to find the information more specifically. The querying fields can be empty if less terms are needed. The two 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)
and: the term following this operator has to be included in the specified field(s)
or: either the preceding or the following term to this operator should occur in the specified field(s)

EXAMPLE: You can click on the "Example" button to load an instance, which could search TP53 in human. The human p53 (PLMD-0003220) will be shown by clicking on the "Submit" button.

(2) Multiple search could be used to find a number of proteins such as a protein list. You can input keyword list, for example, a list of UniProt IDs to search the database. The list should be inputed as one keyword one line.

EXAMPLE: You can click on the "Example" button to load two protein ID including P68363 and P42229. By clicking on the "Submit" button, you can find Signal transducer and activator of transcription 5A and Tubulin alpha-1B chain.

(3) BLAST search could be 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 default is 0.01.

EXAMPLE: You can click on the "Example" button to load the protein sequence of human Histone H4. By clicking on the "Submit" button, you can find the related homologues in other species.