W352 Nucleic Acids Research, 2007, Vol. 35, Web Server issue Figure 1. Sample output of the TFAM Web Server for tRNA genes from Escherichia coli K12. Colors indicate the magnitude and sign of the scores of each sequence to diﬀerent tFAM models. Initiator tRNAs are sorted to the top of the table by clicking on the ‘iMet’ column header. As described more fully in (4), TFAM works by structurally aligning the input sequences with the trusted model sequences using COVE software (15) and tRNA covariance models from (1). It then makes proﬁles of each model class and scores each input sequence according to the log-odds of belonging to a speciﬁc functional class versus belonging to any of the others. This log-odds computation is repeated for every functional class represented in the model. A positive score indicates a match to a particular functional class. The TFAM classiﬁcation of a tRNA sequence is the functional class against which it has the highest score. All results of TFAM computations are available for download from the Web Server including a structural alignment of their sequences (in aligned multi-fasta format) with TFAM classiﬁcations in the description line. The user is also provided a job ID with which she may return to the server for some unspeciﬁed time after visiting the Web Server and recover the results of their computation. Job IDs are not in any way public, so only users with a speciﬁc job ID in hand can recover results from that job. Jobs may be stored on the server for some unspeciﬁed time and then deleted, therefore it is safest to download results after computation. For more data privacy, the user may completely delete the data from our server after down- loading their results. We log user-statistics but do not store any data input to the server for private use. The tRNA structural alignment service of the TFAM Web Server may be useful in its own right. If the TFAM Web Server is used exclusively for this purpose users should additionally cite COVE software (15) and the tRNA covariance models from (1).