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Main topics: ARB: a Short Introduction Glossary Save As ARB intro window (Open, merge, create ARB databases) | Related topics: How to define new import formats NOTES: universal dna NOTES: rdp NOTES: ebi / genbank NOTES: fasta NOTES: dssp NOTES: gde_flat readseq [docindex]
# Import Foreign Data(bases) OCCURRENCE DESCRIPTION Custom import filters NOTES WARNINGS BUGS ## OCCURRENCE
### ARB_INTRO <Create and Import>, ### ARB_NT/File/Import/Import from external format
## 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.
## Custom import filters
### You may create and store your own private import filters in directory '~/,arb_prop/filter'. See ´How to define new import formats´ for information about the import filter definition language.
## NOTES
### Following file formats currently can be detected and loaded: GENBANK, RDP: GENBANK, EBI and FastA ### Several uncommon file formats (including AE2, GCG and DSSP) are kept in directory '$ARBHOME/lib/import/older'. To make them available, copy or symlink them into ''$ARBHOME/lib/import' or into your local filter directory '~/.arb_prop/filter/'. ### To import big new databases into an existing ARB database, convert it to the ARB format first, save and merge it with the ARB_MERGE tool. ### For importing other formats such as PHYLIP or PAUP into an existing ARB database use the 'Import sequences using Readseq' function accessible via the 'File' menu of the 'ARB_NT' main menu. See ´readseq [docindex]´. ### If 'AUTO DETECT' does not find any format, selecting a format by hand most likely wont help you (exception: universal format).
## WARNINGS
### When using 'AUTO DETECT', check if the correct format is detected. RDP files may for instance be identified as GenBank. In such case choose 'rdp.ift' manually.
## BUGS
### 'AUTO DETECT' looks for certain key-words in the files. If it can't find these words, it does not accept the file, even if the file has the correct format. This is especially true for the gcg format.