SilkOrganDB - Silkworm Organelle Proteome Database

An Open-Access Resource for Silkworm Organelle Proteomics

Version: 1.0

Organisms
   

HOW TO USE SILKORGANDB

How to search data?

A powerful search tool is designed on top right of every web page. The tool allows user to perform queries on single or multiple strains, and supports searching for keywords in multiple types, including sequence identifier, description and annotation. For example, user can type "serine protease inhibitor" in the input box and select organism and organelle available, then click the Search button (Fig. 1A). Besides, the search tool can also be used to fetch sequences with given required location information in format of “ID:start..end:strand”, like NW_004582010:1685035..1707241:-. In a result, search results are listed in a table which can be sorted and filtered for further searches, as well as copied, printed and exported in formats of XLS, PDF and JSON, respectively (Fig. 1B). Similarly, clicking on a feature id will bring you to the feature details page (Fig. 1C and Fig. 1D).

How to browse data?

All proteins for each organelle can be accessed from hyperlinks in an organelle picture (Fig. 2A) on the front page. The hyperlink will bring you to a table (Fig. 2C) which lists protein numbers for selected organelle in each organism. And from the number, protein information, including experimental parameters and functional note, can be browsed in a responsive table (Fig. 2D), which can be searched, selected, copied and exported in JSON, XLS and PDF format, respectively. Alternatively, organelle proteins of each organism can also be browsed via an table on the front page(Fig. 2B). By clicking the oganelle name, you can explore the identified proteins for the organelle (Fig. 2D). Clicking a feature ID in the the table demonstrated in figure 2C brings you to a webpage, where details of each feature, like sequence length, molecular weight, genomic position, subcellular localization, gene ontology and publication can be selectively viewed (Fig. 2E).

How to analyze data?

SilkOrganDB provides two tools for analyzing homologous sequences. SilkOrganDB BLAST (Fig. 3A) which is built with latest NCBI BLAST+ and supports searching against multiple target datasets (Fig. 3B). The query can be both sequences in FASTA format and identifiers in the database. BLAST results are given in standard and tabular formats, from which outputs can be further searched, ordered, filtered, printed and exported in multiple formats. Besides, both matched targets and regions can also be directly exported (Fig. 3C).

The other homologous search tool is HMMER (Fig. 4A), which implements methods using probabilistic models called profile hidden Markov models (HMM). Similarly, the results of HMMER are also listed in a responsive table which can be sorted, filtered and exported (Fig. 4B).

How to download data?

Protein sequence for organelles of all organisms can be directly downloaded in bulk via the Downloads drop down menu at the top of every webpage. Clicking the “Datasets” under the menu brings you to a datasets webpage (Fig. 5), from where compressed sequence files in FASTA formt can be downloaded.