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Last update on 04. Dec 2013 .
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Align Sequence

OCCURRENCE

ARB_NT/ARB_EDIT/EDIT/Align Sequence

 

DESCRIPTION

Aligns or realigns selected sequence with the database sequences. The most similar database sequences are found, and the new sequence is aligned with these according to primary and secondary structure similarity.

Choose the 'Align Sequence' item from the 'ARB_EDIT/EDIT' menu to display the 'ALIGNER' window.

Select a sequence by positioning the cursor on the name and double clicking the left mouse button.

Choose the appropriate 'PT_SERVER' database from the menu displayed after pressing the <Search relatives in> button. (For example, to align a 16S-like rRNA select 16s_rrna_aligned.arb.)

Define whether the most closely related species of the database should be marked or not by pressing the <Mark used relatives> button.

Press the <ALIGN> button.

 

NOTES

The search for the most similar sequences is performed by the 'PT-server'. This server needs a special external database for rapid search. This database is not synchronized with the current database and has to be updated from time to time by a computing-time expensive procedure ('ARB_NT/ETC/Probe Admin').

Marking the closest relatives allows manual optimization of the alignment of the new species with its closest relatives.

 

EXAMPLES

None

 

WARNINGS

The aligner version available with the present package often does not properly align short partial sequences.

 

BUGS

The aligner needs lots of computer memory, sometimes more than you have. In this case it may not align some sequences.

The aligner does not align the last 3-6 bases of short sequences correctly. Look at the end of your sequences.