The COMER web server for protein analysis by homology

Summary: Sequence homology is a basic concept in protein evolution, structure and function studies. However, there are not many different tools and services for homology searches being sensitive, accurate and fast at the same time. We present a new web server for protein analysis based on COMER2, a sequence alignment and homology search method that exhibits these characteristics. COMER2 has been upgraded since its last publication to improve its alignment quality and ease of use. We demonstrate how the user can benefit from using it by providing examples of extensive annotation of proteins of unknown function. Among the distinctive features of the web server is the user’s ability to submit multiple queries with one click of a button. This and other features allow for transparently running homology searches—in a command-line, programmatic or graphical environment—across multiple databases with multiple queries. They also promote extensive simultaneous protein analysis at the sequence, structure and function levels.