How to start with Sequences module? - LabCollector

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How to start with Sequences module?

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SUMMARY:

You can check our Knowledgebase on how a module generally looks like.

Follow these steps to access the Sequences module:

1. Open the Sequences module

2. Open a record

1. Open the Sequences module

  • 1. This area will show you the name of the module, the search options, and allow you to add a new record.
      1.1 “Import GenBank Data” option helps you to add the sequences directly from the GenBank site. *Check our KB on how to import data in the plasmid module, the process for sequences is explained in the           KB.
      – 1.2 “Blast new sequence” option helps you to Blast or Megablast a sequence.
    * Check our knowledgeBase on how to search in LabCollector.
  • 2. The   options allow you to export all your search results in HTML, CSV, EXCEL, PDF format. You can also select the field that you want to export.
        Read our KnowledgeBase on what are fields and records.
        The option allows you to memorize all records that can be used further in LabCollector.
  • 3.  The records won’t generally show at first. You need to click on the search icon with an empty search field and you will be able to see all the records.

2. Open a record

  • When you click on a particular record, you will see the below options.

  • A. The record name and details will appear here.
  • B. Options for editing the record will be displayed here. Read our KnowledgeBase records editing options.
  • C. The fields related to the record will be displayed here. Read our KnowledgeBase on what are fields.
  • D. This vertical bar will provide you with the options related to the record.
          

    This icon will display the record as seen in the above image.
    This option will display all the related records. For example, if you have a parent and child samples. Then all the child samples will be shown here. or if you have created a link for this record in other modules, then all the related records will be visible here.
    This option shows you the sequence (5′-3′) & linear map of the sequence with all the annotations in the FASTA view, GB format & formatted view.
    This option helps you manage sequence annotations. For example, if it is a sequence of plasmid then you can add annotations like some restriction sites or promoter regions. You can observe here the start/end & orientation (reverse/forward) of a specific annotation. This means that when you import or create a plasmid, you can choose which annotations you want to see or delete. If you import this sequence in the plasmid module you will see these annotations in the plasmid map.
    This option offers you NCBI Blast tools where you can perform a BLAST in LabCollector, external sites
    This option allows you to edit the sequence. When you upload an associated file you can edit the sequence bases.

    You can see the analysis tab here. This can show you the analysis value over days or hours. You can add your choice of custom fields here.
    *Read our knowledgeBase on how to add custom fields in the analysis tab.

    You can link the record to the Electronic Lab Notebook (ELN is an add-on in LabCollector). You can link the record to a particular experiment that has been performed using the record item. This helps you have a link to where the record item was utilized and the results obtained thereafter.
    This icon connects you to the Workflow (WF) add-on in LabCollector. WF add-on is the one where you can make a flowchart of your process where each step requires supervisor validation. If the record is being used in a WF add-on then you will be able to see its status in WF here.
  • E. Here you can search for the primers in Primers module that hybridize (complementary pairing of the DNA/RNA) with the certain nucleotide of the plasmid at 3′ end. You can choose the number of nucleotides that you want to search for the primers. When you click on “Do”, the browser will open the primers module and show you the list of complementary primers.
  • F. Here you can see all the links that you have created for the record. These links are to the other records in other modules in LabCollector. For example, if you have a plasmid for a specific bacterial strain. Then you can connect the plasmid record from the plasmid module to the bacterial record in strains and cells module. You can add a link from LabCollector by clicking on the option “Add a link” and by click the “Open Treeview” option you can see the links connected to the records. 

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