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Last update on 08. Apr 2009 .
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Import Foreign Data(bases)

OCCURRENCE

ARB_INTRO <Create and Import>, ARB_NT/File/Import/Import sequences and fields (ARB)

 

DESCRIPTION

Reads foreign data(base) formats, creates a new ARB database, and imports the foreign data. A selection of commonly used foreign formats can be automatically identified. Data can be imported from single or multiple files.

Type a source file name to the 'Enter file name of foreign database' subwindow. Use * and ? as multiple and single character wild carts to load a set of files, respectively. Alternatively you may select a file from the directories and files subwindow.

Make a selection whether you want to import

  • a full genome flatfile (in GENBANK or EMBL format) or
  • normal sequence files.

In the second case select the file format from the 'Select foreign database format' subwindow or press the 'AUTO DETECT' button.

If your file type is not in the list and you are only interested in the sequence, try 'universal'.

Enter an 'alignment' name. This allows you to distinguish between different alignments in the same datebase later.

Press the 'GO' button.

 

NOTES

Following file formats currently can be detected and loaded: GENBANK, RDP: GENBANK and AE2, GCG used by GENIUS, FastA.

To import big new databases into an existing ARB database, convert it to the ARB format first, save and merge it with the 'ARB_INTRO <MERGE TWO ARB DATABASES>' tool.

For importing other formats such as PHYLIP or PAUP into an existing ARB database use the 'Import Foreign Formate (using GDE, Readseq)' function accessible via the 'File' menu of the 'ARB_NT' main menu.

If 'AUTO DETECT' does not find any format, selecting a format by hand (except the universal format) will not help you.

 

READSEQ

Alternatively 'readseq' can be used to import sequences. It's also located in 'ARB_NT/File/Import' menu. See ´readseq document index´

 

WARNINGS

!!! Using 'AUTO DETECT', check whether the format is detected correctly. RDP files may be identified as GenBank. In this case choose '.../rdp.ift' manually.

 

BUGS

'AUTO DETECT' look for certain key-words in the files. If it can not find this words, it does not accept the file, even if the file has the correct format. This is especially true for the gcg format.