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Tour: viewMulti Alignment
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viewMultiTCW - View and Query Multiple Species
Start | Clusters | Pairs | Sequences | Alignment | Sequence Details | Annotation Hits
Alignment
Sequence Table | Pairwise | MSAdb | MSA...

Sequence Table

Alignments are only available from the sequence table. However, every table leads to the sequence table:
Sequence view
Sequence view for clusters
Sequence view for pairs
Sequence view for hits
If there are only protein (AA) sequences in the database, only the AA options described below will be available.

Pairwise...

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The Pairwise... drop-down has the options shown on the righe, where all options use dynamic programming for the selected sequence(s).

The "for one pair" options are only enabled if a pair is selected.


AA, CDS and NT alignments of a pair. The text alignment can be viewed by clicking the AA, CDS or NT buttons.


Menu for the CDS text alignment:
Text alignment of the CDS showing matches.
The '|' are mutations in synonymous codons, the '*' mutations in nonsynonymous codons.

MSAdb

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This option is only available for Sequence view for clusters, as the multiple sequence alignment (MSA) is computed per cluster when the database is built.

MSA...

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The MSA... drop-down has the options shown on the right, where all options execute the MSA program for the set of selected sequences.

AA is the translated ORF, CDS is the un-translated ORF, and NT is the entire transcript.

The display is the same as shown above for MSAdb.
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