Search Handbook

Specimen and Sequence Pages

Specimen Page

This window is opened by clicking on a Sample ID in the Record List. It highlights voucher information, taxonomy, collection data, and specimen details about the record. If a record has a BIN assignment, there will be a link to the specific BIN Page within the taxonomic section of the record. Specimen information can be edited by selecting Edit Specimen from the upper right corner of the screen. This button will only be visible to users who have editing access to the specimens.

An interactive Google map is also available. In this map users may zoom in to the exact collection site and, where available, select the street view of the area. This feature can be useful to gain an idea of the habitat conditions at the collection site. Collection locations are displayed on the map based on GPS coordinates only when these are provided in the submission.

Comments and Annotation can be added to the Specimen Page in different forms. There are two buttons available on the form to add a tag or a comment to the record. Comments or tags will be displayed for the whole record, or just for the image. By selecting the Add Tags and Comments button, users may choose to use one for the pre-created tags, create a new tag, or add a personal comment. More information on how and why annotate a record can be found here.

Specimen Page Specimen Data Page

By clicking on the main image, users will open a zoomable copy. This larger image is useful for a more extensive taxonomic examination of the specimen, by being able to zoom in to different parts of the organisms users can identify morphological features which may not be clear at the image's original size. This window will also display the licensing and attribution details for the image, including the email address of the license holder for those who may be interested in using the image.

Specimen Image Image Viewer accessible by clicking on the main image in Specimen Record. Hovering over the image produces a zoomed view of that section of the photo.

Sequence Page

The sequence page is opened by clicking on a Process ID from the Record List for users with sequence viewing permission. This page provides details on the trace file(s) and sequence(s) for the specimen. Where multiple markers were sequenced for the same specimen, individual sequence information can be accessed by using the tabs at the top of the screen. Sequence details include a sequence overview, the nucleotide and amino acid sequence, and an illustrative barcode.

Users are able to automatically run an identification request using the BOLD ID Engine by selecting on of the 4 databases available: Full DB, Species DB, Published DB, and Full Length DB .

Trace files can be viewed by selecting at least one trace file and clicking on the View Trace Files button. This will open a new window which displays information on the traces and quality scores as well as a graphical representation of the chromatograms.

BOLD currently supports a BOLD-LIMS report for samples processed in the Canadian Center for DNA Barcode (CCDB) which provides the user with a report on the progress of a sample, along with details on the protocol used.

If a publication is associated with a record, details on the publication title, authors, and source will be available on this page. By selecting the title of the publication, users will be provided with the details of the article, including publication date and abstract where the information is available. Publications are sequence dependent, which means they are directly associated with a specific marker.

Comments and annotations can be added to the Sequence Page and the Trace Viewer . By selecting the Add Tags and Comments button, users may choose to use one for the pre-created tags, create a new tag, or add a personal comment. More information on how and why annotate a record can be found here.

Edit and Delete Sequences Manually

Nucleotide sequences can now be edited or deleted directly on this page, by users with the adequate permission level. By clicking on Clear Sequence users will be able to remove the full nucleotide sequence from the record; while by clicking on Edit Sequence users will be able to add or remove base pairs in a text box format.

sequence Page Sequence Data Page

Trace files can be viewed by selecting at least one check box in the Sequence Runs in the Sequence Page. Upon submission, it may take up to 24 hours for users to be able to download or view trace files.

By clicking on View Trace Files, a new window will open, which details each trace run along with a graphical representation of the trace's chromatogram. In cases where quality scores for the traces are not provided in the submission package, values will be automatically calculated by BOLD.

Summary statistics on the overall quality scores for each trace are included, along with a visual display of individual quality values for each peak. Users can scroll through the chromatograms in order the interpret the intensity and quality of the traces. Every trace is displayed in the original orientation and direction, so that reverse traces are not displayed in the complementary alignment. By selecting View Sequence users may examine the nucleotide sequence for each individual trace.

Trace Viewer Trace Viewing Page accessed from the Sequence Page

Sequence Editor

The newest version of BOLD introduces a customized, built-in sequence editor. Users now have the ability to view and assemble trace files directly on BOLD. The Sequence Editor tool allows users to call and delete base pairs and then to upload the sequences directly into their records.

Sequence Editor Sequence Editor accessible from the Sequence Page

  • tag_account
  • tag_download
  • tag_specimen
  • tag_image
  • tag_genbank
  • tag_sequence
  • tag_tracefile
  • tag_bin
  • tag_analysis
  • tag_new
  • tag_taxonomy
  • tag_map

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