METHODS

NemChR-DB is a database of nematode G-protein coupled chemoreceptors. To predict NemChRs we used hmmsearch to compare proteins against a database of GPCR Pfam hidden Markov models (HMMs). Matches were then filtered to keep proteins with between 5 and 9 TM domains (GPCRs should have 7TMs) as well as a top hit to nematode chemoreceptor HMM profiles and chemoreceptors from Caenorhabditis elegans

The database is mined from genomes available at WormBase ParaSite Version: WBPS16 (WS279). We plan to add more genomes to the database on a rolling basis, and encourage users to submit requests for new species by clicking the contact button

Data can be viewed under the BROWSE tab which loads a table of NemChR-DB entries

The protein sequence for each entry can be viewed by clicking the green icon to the left of each entry. Once clicked the green icon turns red

Entries can be filtered using the search text-box to find matching terms from within the database

Each entry is linked to an external database where more information related to the putative chemoreceptor can be found. A Transcript name is provided for each entry, as well as the protein length, and molecular weight (KDa)

An expected amino acid value is provided for each protein sequence (ExpAA), when >18 suggests is likely to be a transmembrane (TM) protein. The number of predicted TM domains is provided in the Helices column. The Topology column provides the position of the TM helices that are separated by 'i' if the domain starts on the inside or 'o' if the domain starts on the outside while a signal peptide is given by the position of its h-region separated by n and c; e.g. Topology=i6-27o42-58i reveals that the first TM domain starts on the inside from position 6 to 27, followed by the next TM domain on the outside from position 42 to 58. These values were calculated using TMHMM and Phobius

Filtered data can be copied and pasted to another application, or downloaded directly into Microsoft Excel format by clicking the Copy or Excel buttons respectively. Also, the number of visible rows can be set by the user by clicking the Show 25 rows button

Users can interrogate NemChR-DB using local Blast executables under the BLAST tab by dropping raw protein sequence into the query text-box and selecting the output format and database. More details about local Blast executables are detailed in the following paper

Under the TM FINDER tab, users can enter raw protein sequence into the query text-box, and click submit to return a graphic result depicting all predicted TM domains within the user-supplied protein. TM domains are predicted using TMHMM