Orthomap identifies putative bioinformatic orthologs between two selected genomes via a best BLAST analysis. Namely, Orthomap looks up the results of a pairwise BLAST analysis between the two genomes for the set of inputted loci. The pairs of loci that pass the significance threshold corresponding to an E-value of 10^-5 are returned.

What does the "reciprocal" option do?

Reciprocal best BLAST is one well established method of determining orthologs between two genomes. If this option is selected, Orthomap ensures that for a given inputted isoform the resultant isoform is both the best match for the input and has the input as its own best match.

How should I cite Orthomap?

You can use the original article in which Element was released.

Mockler TC, Michael TP, Priest HD, Shen R, Sullivan CM, Givan SA, McEntee C, Kay S, Chory J THE DIURNAL PROJECT: Diurnal and circadian expression profiling, model-based pattern matching and promoter analysis. Cold Spring Harb Symp Quant Biol. 2007;72:353-63. PMID: 18419293

Who should I contact to ask questions or give feedback regarding Orthomap?

You can send an email to info@mocklerlab.org with Orthomap in the title.