For now, we can suggest some alternatives:
- BiSearch: can be used for primer searches (MSP or bisulfite primers) and is ideal to check whether primers are specific; genomic location of the amplicon is given and supports multiple organisms
- For really mapping/aligning bisulfite converted sequences, there are mapping tools, able to deal with the bisulfite conversion such as BatMeth: http://genomebiology.com/2012/13/10/R82.
Other tools are very similar (BSMAP/BS Seeker/BisMark).Unfortunately, these mappers are not available online and thus require an installation (and the creation of the genome indexes etc.). As a replacement of the inefficient BLAST, we could use such a tool and present an web-interface to it where MethBLAST is now. We will investigate the possibilities to do so.