Filename                                    Description
--------                                    -----------
jp_lyRAszr.align                            PSIBLAST alignment with gaps and redundancy removed in FASTA format
jp_lyRAszr.als                              Alscript command file. Used to generate PS/PDF outputjp_lyRAszr.blast.gz                         PSIBLAST output (compressed)
jp_lyRAszr.coils.csv                        The output from coils in CSV format
jp_lyRAszr.coilseq.lupas_14                 The output from coils using a window length of 14
jp_lyRAszr.coilseq.lupas_21                 The output from coils using a window length of 21
jp_lyRAszr.coilseq.lupas_28                 The output from coils using a window length of 28
jp_lyRAszr.concise                          The prediction in pseudo-CSV format, including the coiled-coil prediction, solvent accessiblity and the sequence alignment
jp_lyRAszr.concise.blc                      A BLC file of the prediction and alignment
jp_lyRAszr.concise.pdf                      A PDF file of the prediction and alignment
jp_lyRAszr.fasta                            Input query sequence in FASTA format
jp_lyRAszr.full_MSA.fasta                   The full multuple sequence alignment before JPred filters. Gaps/insertions shown. FASTA format.
jp_lyRAszr.hmm                              The HHMer2 profile of the alignment
jp_lyRAszr.html                             A HTML file of the prediction and alignment
jp_lyRAszr.input                            Your raw input
jp_lyRAszr.jalview                          A Jalview annotation file to be read in with the .align file to view the predictions in Jalview
jp_lyRAszr.jnet                             The output from Jnet
jp_lyRAszr.profile                          PSIBLAST profile
jp_lyRAszr.pssm                             PSIBLAST PSSM in a format for Jnet
jp_lyRAszr.seq                              Your sequence
jp_lyRAszr.simple.html                      The brief HTML output of the query sequence and prediction only
jp_lyRAszr.svg.html                         A Jalview generated SVG file with summary of the results.