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These options control formatting of alignments in results pages. The default is HTML, but other formats (including plain text) are available. PSSM and PssmWithParameters are representations of Position Specific Scoring Matrices and are only available for PSI-BLAST. The Advanced view option allows the database descriptions to be sorted by various indices in a table.


Choose how to view alignments. The default "pairwise" view shows how each subject sequence aligns individually to the query sequence. The "query-anchored" view shows how all subject sequences align to the query sequence. For each view type, you can choose to show "identities" (matching residues) as letters or dots. more...

  • Graphical Overview: Graphical Overview: Show graph of similar sequence regions aligned to query. more...
  • NCBI-gi: Show NCBI gi identifiers.
  • CDS feature: Show annotated coding region and translation. more...
  • Masking Character: Display masked (filtered) sequence regions as lower-case or as specific letters (N for nucleotide, P for protein).
  • Masking Color: Display masked sequence regions in the given color.
  • Descriptions: Show short descriptions for up to the given number of sequences.
  • Alignments: Show alignments for up to the given number of sequences, in order of statistical significance.
  • Line lenghth: Number of letters to show on one line in an alignment.

Show only sequences with expect values in the given range. more...


Show only sequences with percent identity values in the given range.

  • Format for PSI-BLAST: The Position-Specific Iterated BLAST (PSI-BLAST) program performs iterative searches with a protein query, in which sequences found in one round of search are used to build a custom score model for the next round. more...
  • Inclusion Threshold: This sets the statistical significance threshold for including a sequence in the model used by PSI-BLAST to create the PSSM on the next iteration.