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Search Index   Help   Support   Email   Reference Biology Reference Index | Dictionaries | Language Resources | Encyclopedias | eTexts | Map Resources | Libraries | Periodicals | Forum | Chat Page 1 | 2 | 3 | 4 SWISS2D Page SWISS3D Image TBASE Citation Database UIP Biology Department USC Sequence Alignment Server Alignment parameters Type of alignment: Local Global Fit Overlap Self-repeats Tandem repeats Scoring metric (Distance only with Global and Fit scoring): Similarity Distance Type of match/mismatch scoring (Profile only with Fit scoring): Single Score Penalty Matrix Profile Matrix Match score, if Single-score scoring chosen (Similarity scoring only): Mismatch penalty, if Single-score scoring chosen: Alpha, for gap penalty g(k) = alpha + beta*(k-1): Beta, for gap penalty g(k) = alpha + beta*(k-1): Penalty Matrix type (if Penalty Matrix scoring chosen above): Pre-defined matrix (see list of available matrices): User-supplied matrix (supply in BLAST format): First sequence (paste your sequence here, with title line, in FASTA format): Second sequence (paste your sequence here, with title line, in FASTA format); or Profile Matrix if Profile and Fit options were chosen (supply in profile format): Reverse-complement the second sequence (if nucleotide)? No Yes Output parameters Print alignment (otherwise, a space-efficient model is used)? Yes No Number of alignments to print, if Local or Fit chosen (if printing alignments): Preferred traceback direction for indels (if printing alignment): Upper Lower Flip Print overlaps from both sequence ends rather than best one (Overlap only)? No Yes Yale Journal of Biology and Medicine All files Full text of journals only Page 1 | 2 | 3 | 4

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