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Search Tutorial

Please read the search-related Opens internal link in current windowFAQs prior to the search tutorial.

Basic Search Functions

  1. Search for Accession number

  2. Search for a Range of Accession Numbers

  3. Search for Multiple Accession numbers

    Space separated lists are also accepted. If a version is given with the accession ("AJ579313.1") the version is ignored.

  4. Search for Organism name restricted to sequences in the SILVA SSURef dataset

    By clicking on 'Add found sequences to cart' the sequences are ready for Download. The Cart shows the total number of sequences in the cart (4). Show shows all sequences in the cart. Clear removes all sequences from the cart. Clicking on the table headers, e.g. sequence length, sorts the results.

  5. Clicking on the 'browser symbol' in Options links to the Taxonomic Browser. The percentages shown in brackets indicate the coverage of the sequences in the respective phylogenetic group. In this case, 8.2% of the sequences of the genus Nevskia are in the cart.

  6. Search for NCBI tax ID

    Only single values are supported for the NCBI tax ID, i.e. you can only search for one tax ID at the time. However, you can use the cart (see Combined Search Functions below) to combine multiple searches into one final search result. The result is limited to the sequences which are directly assigned to the specified taxon. Thus, searching for higher-level taxa like Bacteria (tax ID 2) will give no results.

Advanced Search Functions

  1. Search for sequences within a specific Taxonomic group and have constraints on sequence length, sequence and alignment quality

  2. Search for sequences within a specific Taxonomic group that have been deposited in EMBL after 01 January, 2009 and have constraints on sequence length and sequence quality

  3. Search for sequences within a specific Taxonomic group that have been deposited in EMBL after 04 August, 2009 and have constraints on sequence length and sequence quality

  4. Search for sequences deposited by a specific Author and have constraints on sequence length and quality

  5. Search for sequences from a specific Publication and have constraints on sequence length and quality. The number in publication ID can be the Pubmed ID or the DOI

  6. Search for all sequences from cultured strains. First search for all type strains using the search term [T] and click on Add found sequences to cart.

    Next search for all cultured strains according to the StrainInfo project using s[C] as search term and add them to your cart as well. Now your cart contains all cultured strains.

    To filter those type strains by e.g. sequence quality you enter the search criteria as normal but restrict the search to your cart by selecting my Cart. Now you have the option to remove the found sequences from the cart (i.e. retain only the low quality sequences) or replace the current cart with the found sequences (i.e. discard the low quality sequences).

  7. Search for all genomes that are typestrains. 599 accession numbers representing 1885 rRNA sequences - due to multiple operons - are found.

  8. Search for all sequence in the SILVA SSURef dataset that do not have a perfect pintail score (<100), but only those for which pintail results are available (>-1)

Combined Search Functions

  1. You want to add all Archaeoglobus sequences from the SILVA Ref tree to the cart. First search for Archaeoglobus. Click on the browser symbol of an entry in the result list -> browser opens. 

  2. Add all sequences by clicking on the cart symbol next to Archaeoglobus. The cart now contains 43 sequences. 

  3. Click on Show to go back to the Search page. For download, you only want to keep sequences that are longer than 1500 bases. Search for all sequences in the Cart that are longer than 1500 bases:

    and replace the sequences in the cart with the search result by clicking on 'Replace current cart with found sequences'.

    This leaves 1 sequence in the cart for Download.

Download Sequences in Cart

  1. Select individual sequences or add all sequences to your cart for download.
  2. Click on Download and the following menu will pop up:

  3. Select the output format (ARB file or Multi-Fasta file) and if the file should be compressed using Zip (Windows) or tar (Linux). For the FASTA format the alignment of the exported sequences can be controlled. Select with gaps to export aligned sequences, common gaps to suppress all common gaps of the exported sequences or without gaps for unaligned sequences.
  4. Click on: Start export
  5. The files can be retrieved on the TaskManager page. Select the export you want to download and click on Download file.
  6. Proceed by e.g merging your ARB file with your personal ARB database see Opens internal link in current windowFAQs