DNA search

Disclaimer - read before using search tool

This DNA sequence search tool is designed to assist users in verifying the identity of spider species. The tool searches for an exact match between the input sequence and the reference database, which contains nucleotide sequence data from fully vouchered individuals collected recently from table grapes in California. Each sequence in the database was obtained using chelicerate paired primers designed by Barrett and Hebert (2005) or the universal metazoan Folmer primers (Folmer et al 1994) to amplify a 680 base pair portion of the mitochondrial gene cytochrome c oxidase subunit I (COI), commonly known as the DNA barcode region. The search tool assumes that the input sequence was generated using primers designed to amplify the COI barcode region, the sequence has been properly trimmed, and the primer sequences removed. A sequence that contains primers or is too long will not return a match regardless of the specimen identity. Input sequences must be verified to be of sufficient length, to be free of primers, and to not contain excessive ambiguous data. A Verify Sequence button allows users to check for problems in the DNA sequence before submitting it to the database.

The search tool will return the name and description of species if a match is found. A message that the sequence is consistent with one more means that the input sequence exactly matches one of the reference sequences. This information can be used to assist with specimen identity; however, it is possible that different species share identical barcode region sequences and information obtained from the search tool should be used with caution. A message that the sequence is not consistent with any haplotypes in the database means that the input sequence does not exactly match any of the reference sequences. This could be due to errors in the input sequence, a failure to sample all haplotypes of a particular species, or differences in species identity, and this information should be used with caution.

Search DNA sequences

Before using the DNA search tool, please read the disclaimer at the top of the page.

Search strings can contain any of the standard nucleotide codes (A, G, C, T, and also N, R, Y, W, S, M, K, B, H, D, V). Sequences must be properly trimmed with primers removed and must be less than 680bp in length. To minimize false positives, sequences should not contain an excess of ambiguous data (long strings of NNNNNs). To verify that your sequence meets these criteria, click Verify Sequence. To view haplotypes that are consistent with your sequence, click Submit Query.

NOTE: The DNA search tool functions correctly in most browsers. However, the DNA search tool does not function correction in the Safari or Google Chrome web browsers. Example data is provided below to verify that your web browser is compatible with the DNA search tool.

Enter search string here. Please make sure that your sequence does not have any line breaks or return characters at the end of lines:


Example Data

The following sequences are provided as examples for users to verify functionality of the DNA search tool with their web browser and to demonstrate use of the Verify Sequence and Submit Query buttons. Copy and paste the following sequences into the DNA search tool and verify that the tool returns the appropriate message.

This sequence should verify correctly:

ATTATATTTTATTTTTGGTATTTGAGCAGGTATAGTAGGAACATCCCTAAGATTATTAATTCGAGCRGAATTAGGAAAYCCTGGATCATTAATTGGA

This sequence should not verify (HCO primer not removed):

CAGAATTAGNNNNCCCTRRATVATTAATTGGAGATGATCAAATTTATAATACTATTGTCACAGCTCATGBTATACTTCAGGATGACCAAAAAATCAN

This sequence should not verify (excessive ambiguous data):

ANGTNTAGTAGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCCTRRATVATTAATTGGAGATGATCAAATTTATAATACTATTGTN

This sequence should not verify (too short):

ANGTNTAGTAGGWWCA