Searching for ORFs (GO)

Search By ID (Board)

  1. Open the 'Search By ID (Board)' popup.
    • In the Main Window, on the Search menu's ORF (GO) submenu, click By ID (Board), or
    • In the Main Window, select ORF (GO) from the drop-down list on the button bar, then click on the appropriate 'magnifying glass' button, or
    • To replace a previous search by a new one in an active ORF(s) View in the Board, on the Board's Search menu click By ID.
  2. Set the search criteria in 'Search by ID (Board)' popup.
    • Search ORFs in determines if All ORFs, or the ones uploaded by the Default Lab Only will be searched.
    • Source Organism is a drop-down list of the organisms from the Lab Resources Source Organism resource.
    • Cluster Seed is a drop-down list of the seeds for the clusters to which the ORFs belong.
    • Gene locus is the specific location of the gene sequence on a chromosome. Wildcard Characters are allowed.
    • Filter by WorkGroup allows one to restrict the search to ORFs that are in at least one workgroup, or those that were not added to any.
    • Protein Name is the name of the protein. Wildcard Characters are allowed.
    • Lab ID is a lab defined ID for the ORF. Wildcard Characters are allowed.
    • Main ID is the main ID for the ORF. Wildcard Characters are allowed.
    • Source DB Start Date is the earliest date the Source Database was created, or when the ORFs were uploaded. To set it to an '*', click on it, then clear, or enter an '*', into any of the Year, Month or Day fields.
    • Source DB End Date is the latest date the Source Database was created, or when the ORFs were uploaded. To set it to an '*', click on it, then clear, or enter an '*', into any of the Year, Month or Day fields.
  3. Click Search in the search popup.

Note

Search By Content (Board)

  1. Open the 'Search By Content (Board)' popup.
    • In the Main Window, on the Search menu's ORF (GO) submenu, click By Content (Board) or,
    • To replace a previous search by a new one in an active ORF(s) View in the Board, on the Board's Search menu click By Content.
  2. Set the search criteria in 'Search by Content (Board)' popup.
    • Search ORFs in determines if All ORFs, or the ones uploaded by the Default Lab Only will be searched.
    • Source Organism is a drop-down list of the organisms from the Lab Resources Source Organism resource.
    • Cluster Seed is a drop-down list of the seeds for the clusters to which the ORFs belong.
    • Gene locus is the specific location of the gene sequence on a chromosome. Wildcard Characters are allowed.
    • Filter by WorkGroup allows one to restrict the search to ORFs that are in at least one workgroup, or those that were not added to any.
    • Protein Name is the name of the protein. Wildcard Characters are allowed.
    • Return (rows) is the maximum number of ORFs that will be returned.
    • Sort by: allows one to sort the resulting ORFs by Target Score or Heat.
    • Filter by Error in Gene Code allows one to restrict the search to ORFs with No error, or to the Erroneous ones.
    • Residue Length is the length of the Amino Acid Sequence. The comparison operator options are in a drop-down list.
    • No of Introns is the number of Introns in the Amino Acid Sequence. The comparison operator options are in a drop-down list.
    • No of Cys is the number of Cysteines in the Amino Acid Sequence. The comparison operator options are in a drop-down list.
    • Signal Peptide Length is the length of the Signal Peptide Sequence. The comparison operator options are in a drop-down list.
    • Source DB Start Date is the earliest date the Source Database was created, or when the ORFs were uploaded. To set it to an '*', click on it, then clear, or enter an '*', into any of the Year, Month or Day fields.
    • Source DB End Date is the latest date the Source Database was created, or when the ORFs were uploaded. To set it to an '*', click on it, then clear, or enter an '*', into any of the Year, Month or Day fields.
    • Structure Class is a multi-selection checkbox that contains all the protein structure classes that can be excluded from the search.
  3. Click Search in the search popup.

Note

Search By Criteria (Board)

  1. Open the 'Search By Criteria (Board)' popup.
    • In the Main Window, on the Search menu's ORF (GO) submenu, click By Criteria (Board) or,
    • To replace a previous search by a new one in an active ORF(s) View in the Board, on the Board's Search menu click By Criteris.
  2. Set the search criteria in 'Search by Criteria (Board)' popup.
    • Content tab replicates the 'Search by Content (Board)' criteria.
      • Search ORFs in determines if All ORFs, or the ones uploaded by the Default Lab Only will be searched.
      • Source Organism is a drop-down list of the organisms from the Lab Resources Source Organism resource.
      • Cluster Seed is a drop-down list of the seeds for the clusters to which the ORFs belong.
      • Gene locus is the specific location of the gene sequence on a chromosome. Wildcard Characters are allowed.
      • Filter by WorkGroup allows one to restrict the search to ORFs that are in at least one workgroup, or those that were not added to any.
      • Protein Name is the name of the protein. Wildcard Characters are allowed.
      • Return (rows) is the maximum number of ORFs that will be returned.
      • Sort by: allows one to sort the resulting ORFs by Target Score or Heat.
      • Filter by Error in Gene Code allows one to restrict the search to ORFs with No error, or to the Erroneous ones.
      • Residue Length is the length of the Amino Acid Sequence. The comparison operator options are in a drop-down list.
      • No of Introns is the number of Introns in the Amino Acid Sequence. The comparison operator options are in a drop-down list.
      • No of Cys is the number of Cysteines in the Amino Acid Sequence. The comparison operator options are in a drop-down list.
      • Signal Peptide Length is the length of the Signal Peptide Sequence. The comparison operator options are in a drop-down list.
      • Source DB Start Date is the earliest date the Source Database was created, or when the ORFs were uploaded. To set it to an '*', click on it, then clear, or enter an '*', into any of the Year, Month or Day fields.
      • Source DB End Date is the latest date the Source Database was created, or when the ORFs were uploaded. To set it to an '*', click on it, then clear, or enter an '*', into any of the Year, Month or Day fields.
      • Structure Class is a multi-selection checkbox that contains all the protein structure classes that can be excluded from the search.
    • Criteria tab allows one to specify constraints for primer determination.
      • Min. Primer Length is the minimum length of the calculated primer.
      • Max. Primer Length is the maximum length of the calculated primer.
      • Min. Tm is the minimum melting temperature of the calculated primer C.
      • Max. Tm is the maximum temperature of the calculated primer C.
      • Tm Calculation allows one to select how the melting temperature, in C, is calculated.
        • Simple uses the standard approximation, where Tm = 2 * (#A + #T) + 4 * (#G + #C). # is the 'number of' operator.
        • Not So Simple uses the Simple approximation for sequences shorter than 14 nucleotides, and Tm = 64.9 + 41 * (#G + #C - 16.4) / (#A + #T + #G + #C) otherwise. # is the 'number of' operator.
      • 5' Prefix is a drop-down list of prefix sequences from the Lab Resources 5' Prefix resource that can be added to the 5' primer.
      • 3' Prefix is a drop-down list of prefix sequences from the Lab Resources 3' Prefix resource that can be added to the 3' primer.
      • Limit to 45 Bases allows limiting the maximum length of the primer with an optional prefix to 45 nucleotides.
      • Skip Start Codon allows skipping the start codon of the ORF, if it exists, for primer calculation.
      • Skip Stop Codon allows skipping the stop codon of the ORF, if it exists, for primer calculation.
      • Check for G or C end if checked, the calculated primers will end with a G or C.
      • Check GC Content 40-60% if checked, the GC content of the calculated primers will be between 40% and 60%.
      • Check pair Tm difference < 5 if checked, the difference of the melting temperatures for the calculated 5' and 3' primer pair will be less than 5C.
      • Check for G or C end run > 3 in 5 if checked, primers for which the sum of the G and C nucleotides among the last five is bigger than three will be rejected.
      • Check for runs > 4 if checked, primers that contain more than four consecutive nucleotides of the same kind at any place will be rejected.
      • Check for di-nucleotide runs > 4 if checked, primers that contain more than four consecutive di-nucleotide runs will be rejected.
      • Restriction is a multi-selection checkbox that contains all the restriction enzymes defined in Lab Resources Plasmid Components Restriction resource. Only those ORFs will be returned whose nucleotide sequence contains all the selected Present restrictions, and doesn't contains any of the selected Not Present restrictions.
  3. Click Search to initiate the search.

Note

Search By Characteristics (Board)

  1. Open the 'Search By Characteristics (Board)' popup.
    • In the Main Window, on the Search menu's ORF (GO) submenu, click By Characteristics (Board), or
    • A previous search can be replaced by a new one by right-clicking on an ORF (GO) node in the Search Results Tree and selecting By Characteristics (Board).
  2. Set the search criteria in 'Search by Characteristics (Board)' popup.
    • Search ORFs in determines if All ORFs, or the ones uploaded by the Default Lab Only will be searched.
    • Source Organism is a drop-down list of the organisms from the Lab Resources Source Organism resource.
    • Cluster Seed is a drop-down list of the seeds for the clusters to which the ORFs belong.
    • Gene locus is the specific location of the gene sequence on a chromosome. Wildcard Characters are allowed.
    • Filter by WorkGroup allows one to restrict the search to ORFs that are in at least one workgroup, or those that were not added to any.
    • Residue Length is the length of the Amino Acid Sequence. The comparison operator options are in a drop-down list.
    • Gcode Length is the length of the Genetic Code. The comparison operator options are in a drop-down list.
    • No of Introns is the number of Introns in the Amino Acid Sequence. The comparison operator options are in a drop-down list.
    • No of Cys is the number of Cysteines in the Amino Acid Sequence. The comparison operator options are in a drop-down list.
    • Mol. weight is the molecular weight of the Amino Acid Sequence. The comparison operator options are in a drop-down list.
    • pI is the isoelectric point estimate for the Amino Acid Sequence. The comparison operator options are in a drop-down list.
    • Transmembrane Segments is the number of transmembrane segments in the ORF. The comparison operator options are in a drop-down list.
    • Heat is the 'hotness' of an ORF based on the number of attached database references. The comparison operator options are in a drop-down list.
    • Compound Operator allows one to select the logical operator AND or OR to be used between the search criteria. If AND is selected, only those ORFs will be returned that fit the search criteria. If OR is selected, those ORFs will be returned that fit at least one of them.
    • Source DB Start Date is the earliest date the Source Database was created, or when the ORFs were uploaded. To set it to an '*', click on it, then clear, or enter an '*', into any of the Year, Month or Day fields.
    • Source DB End Date is the latest date the Source Database was created, or when the ORFs were uploaded. To set it to an '*', click on it, then clear, or enter an '*', into any of the Year, Month or Day fields.
  3. Click Search in the search popup.

Note

Search By Sequence (Board)

  1. Open the 'Search By Sequence (Board)' popup.
    • In the Main Window, on the Search menu's ORF (GO) submenu, click By Sequence (Board), or
    • To replace a previous search by a new one in an active ORF(s) View in the Board, on the Board's Search menu click By Sequence.
  2. Set the search criteria in 'Search by Sequence (Board)' popup.
    • Search ORFs in determines if All ORFs, or the ones uploaded by the Default Lab Only will be searched.
    • Type allows one to select the sequence type, Amino Acid or Nucleotide.
    • Sequence is the exact sequence that will be matched.
  3. Click Search in the search popup.

Note

Search By Action (Board)

  1. Open the 'Search By Action (Board)' popup.
    • In the Main Window, on the Search menu's ORF (GO) submenu, click By Action (Board), or
    • To replace a previous search by a new one in an active ORF(s) View in the Board, on the Board's Search menu click By Action.
  2. Set the search criteria in 'Search by Action (Board)' popup.
    • Postion determines the position of the action one is searching for in time. Any will target all the actions attached to an ORF, while Last targets only the last one.
    • Labfund is a drop-down list of various sources of funding maintained by the lab master.
    • Start Date is the earliest date the Action was added to an ORF. To set it to an '*', click on it, then clear, or enter an '*', into any of the Year, Month or Day fields.
    • End Date is the latest date the Action was added to an ORF. To set it to an '*', click on it, then clear, or enter an '*', into any of the Year, Month or Day fields.
    • Source Organism is a drop-down list of organisms maintained by the lab master.
    • Action Lab Protocol is a drop-down list of lab protocols maintained by the lab master.
    • Include Retired Actions controls if the retired Actions will be shown in the Action field for the Lab Protocol selected in Action Lab Protocol.
    • Action Present Match allows one to select the logical operator AND or OR to be used for matching the actions attached to an ORF. If AND is selected, only those ORFs will be returned that have all of the selected Present Actions attached. If OR is selected, those ORFs will be returned that have at least one of the selected Present Actions attached.
    • Action Not Present Match allows one to select the logical operator AND or OR to be used for matching the actions not attached to an ORF. If AND is selected, only those ORFs will be returned that don't have any of the selected Not Present Actions attached. If OR is selected, those ORFs will be returned that don't have at least one of the selected Not Present Actions attached.
    • Action is a multi-selection checkbox that contains all the Actions associated with the Lab Protocol selected in Action Lab Protocol.
  3. Click Search in the search popup.

Note

Search By DB Reference (Board)

  1. Open the 'Search By DB Reference (Board)' popup.
    • In the Main Window, on the Search menu's ORF (GO) submenu, click By DB Reference (Board), or
    • In the Main Window, select ORF (GO) from the drop-down list on the button bar, then click on the appropriate 'magnifying glass' button, or
    • To replace a previous search by a new one in an active ORF(s) View in the Board, on the Board's Search menu click By DB Reference.
  2. Set the search criteria in 'Search by DB Reference (Board)' popup.
    • Search ORFs in determines if All ORFs, or the ones uploaded by the Default Lab Only will be searched.
    • Source Organism is a drop-down list of the organisms from the Lab Resources Source Organism resource.
    • Cluster Seed is a drop-down list of the seeds for the clusters to which the ORFs belong.
    • Gene locus is the specific location of the gene sequence on a chromosome. Wildcard Characters are allowed.
    • Filter by WorkGroup allows one to restrict the search to ORFs that are in at least one workgroup, or those that were not added to any.
    • DB Name is an editable drop-down list that contains the System Resources URL Base Names of various public genomic and proteomic databases. Wildcard Characters are allowed.
    • DB ID is an ID from the DB Name space. Wildcard Characters are allowed.
    • DB Start Date is the earliest date associated with the database reference. To set it to an '*', click on it, then clear, or enter an '*', into any of the Year, Month or Day fields
    • DB End Date is the latest date associated with the database reference. To set it to an '*', click on it, then clear, or enter an '*', into any of the Year, Month or Day fields.
    • Heat is the 'hotness' of an ORF based on the number of attached database references. The comparison operator options are in a drop-down list.
  3. Click Search to initiate the search.

Note

Search By DB Reference List (Board)

  1. Open the 'Search By DB Reference List (Board)' popup.
    • In the Main Window, on the Search menu's ORF (GO) submenu, click By DB Reference List (Board), or
    • To replace a previous search by a new one in an active ORF(s) View in the Board, on the Board's Search menu click By DB Reference List.
  2. Set the search criteria in 'Search by DB Reference List(Board)' popup.
    • Search ORFs in determines if All ORFs, or the ones uploaded by the Default Lab Only will be searched.
    • DB Name is an editable drop-down list that contains the System Resources URL Base Names of various public genomic and proteomic databases. Wildcard Characters are allowed.
    • DB ID List is the list of IDs from the DB Name space. The IDs in the list can be separated by space, tab, comma, semicolon, or end of line.
  3. Click Search in the search popup.

Note

Search By List (Board)

  1. Open the 'Search By List (Board)' popup.
    • In the Main Window, on the Search menu's ORF (GO) submenu, click By List (Board), or
    • In the Main Window, select ORF (GO) from the drop-down list on the button bar, then click on the appropriate 'magnifying glass' button, or
    • To replace a previous search by a new one in an active ORF(s) View in the Board, on the Board's Search menu click By List.
  2. Set the search criteria in 'Search by List' popup.
    • DB# List is the list of ORF Database Nos. The numbers in the list can be separated by space, tab, comma, semicolon, or end of line. Alternatively, if there are DBNo List (LI) records for ORFs, they can be selected from the dropdown list.
  3. Click Search in the search popup.

Note

Search By Linked Item List (Board)

  1. Open the 'Search By By Linked Item List (Board)' popup.
    • In the Main Window, on the Search menu's ORF (GO) submenu, click By Linked Item List (Board), or
    • To replace a previous search by a new one in an active ORF(s) View in the Board, on the Board's Search menu click By Linked Item List.
  2. Set the search criteria in 'Search by Linked Item List (Board)' popup.
    • Item Type is a drop-down list of Sesame Items to which an ORF can be linked.
    • Item Nos is the list of Sesame Item Database Nos selected in Item Type. The numbers in the list can be separated by space, tab, comma, semicolon, or end of line. Alternatively, if there are DBNo List (LI) records for the selected Sesame Itemn, they can be selected from the dropdown list.
  3. Click Search in the search popup.

Note

Search By Sequence

  1. Open the 'Search By Sequence' popup.
    • In the Main Window, on the Search menu's ORF (GO) submenu, click By Sequence, or
    • A previous search can be replaced by a new one by right-clicking on an ORF node in the Search Results Tree and selecting By Sequence.
  2. Set the search criteria in 'Search by Sequence' popup.
    • Search ORFs in determines if All ORFs, or the ones uploaded by the Default Lab Only will be searched.
    • Type allows one to select the sequence type, Amino Acid or Nucleotide.
    • Sequence is the exact sequence that will be matched.
  3. Click Search in the search popup.

Note

Search By List

  1. Open the 'Search By List' popup.
    • In the Main Window, on the Search menu's ORF (GO) submenu, click By List, or
    • In the Main Window, select ORF (GO) from the drop-down list on the button bar, then click on the appropriate 'magnifying glass' button, or
    • A previous search can be replaced by a new one by right-clicking on a ORF (GO) node in the Search Results Tree and selecting By List.
  2. Set the search criteria in 'Search by List' popup.
    • DB# List is the list of ORF Database Nos. The numbers in the list can be separated by space, tab, comma, semicolon, or end of line. Alternatively, if there are DBNo List (LI) records for ORFs, they can be selected from the dropdown list.
  3. Click Search in the search popup.

Note

Search By Linked Item List

  1. Open the 'Search By By Linked Item List' popup.
    • In the Main Window, on the Search menu's ORF (GO) submenu, click By Linked Item List, or
    • A previous search can be replaced by a new one by right-clicking on a ORF node in the Search Results Tree and selecting By Linked Item List.
  2. Set the search criteria in 'Search by Linked Item List' popup.
    • Item Type is a drop-down list of Sesame Items to which an ORF can be linked.
    • Item Nos is the list of Sesame Item Database Nos selected in Item Type. The numbers in the list can be separated by space, tab, comma, semicolon, or end of line. Alternatively, if there are DBNo List (LI) records for the selected Sesame Itemn, they can be selected from the dropdown list.
  3. Click Search in the search popup.

Note

See also