How to Use PSSM Sequence Alignment

Upload profile.json from PSSM Generation and add one or more ungapped candidate sequences. Local alignment reports the highest scoring positive region; global alignment spans both inputs. Candidates are ranked by raw profile score.

The service uses affine gaps with a cost of Gap Open + (k - 1) × Gap Extend bits for a gap of length k. Defaults are five bits to open and one to extend. B/Z/J/X scores marginalize over possible residues; X contributes zero bits. The alignment viewer reports profile and candidate coordinates, including gaps. Original MSA/query coordinates remain available in the downloadable per-position table. Per-residue scores omit gap penalties; the total alignment score includes them. No positive local alignment produces an empty alignment and zero score. Ranking different lengths by raw score can favor longer alignments; inspect spans and support before selecting candidates. Scores are log-odds in bits, with no calibrated E-values or PSI-BLAST equivalence.

Reading and downloading results

Upload the full-precision profile.json from PSSM Generation. alignments.csv ranks candidates by decreasing total score, reports the selected mode and inclusive spans, and displays both gapped strings. Rank 1 is the highest raw score; tied ranks do not imply biological differences. Profile Start and Profile End index retained profile rows, while Sequence Start and Sequence End refer to the full ungapped candidate. They do not index the displayed gapped string.

alignment_positions.csv maps each gapped alignment column to its retained profile position, original MSA match column, original query residue and candidate residue. Coordinates in CSV and the viewer are one-based; a blank coordinate indicates a gap or an unassigned query. A3M insertion residues count in original query numbering although they have no profile row. Profile Residue is the profile consensus, which may differ from the original query. Residue Score is a contribution before gap penalties, so adding only the displayed residue scores will not reproduce a gapped total. Zero-probability matches can score -inf; global alignment fails when no finite alignment exists. Hover headers or cells for detailed definitions.

Submit up to 100 candidates, each up to 10,000 residues. Large profile/candidate combinations may need to be split into smaller batches; the accepted limits are 1 million profile-by-candidate positions per pair, 5 million per batch and 100,000 combined profile and candidate residues.

• Reusable profiles: Retain full-precision probabilities and source coordinates.
• Clear scoring: Interpret profile scores in bits.
• Downloadable results: Inspect tables and alignment details.