Base Pair Frequency Section Help File

Last modified on 27 July 2001.

Help Window:

Help on table headings and more detailed information about interactions will appear here when you select an appropriate link.

Help for "Base Pair Lists"

HEI:

Helical Element Identifier. A helical element is the largest possible helix which contains no multi-stem loop structure. The numerical identifier corresponds to the lowest numbered nucleotide (in the reference sequence) within a helical element. A comment is associated with those helical elements that have a link. Background colors are assigned as follows:

• White: Element contains secondary and tertiary base pairs.
• Yellow: Element contains only tertiary structure base pairs.

Base Pair Position Numbers:

• Nucleotide numbers refer to the appropriate reference sequence:
  • 5S rRNA
  • 16S rRNA
  • 23S rRNA
  • Group I Intron RNA
  • Group IIA Intron RNA
  • Group IIB Intron RNA
  • tRNA
• Selecting a base pair link presents the appropriate base pair frequency table in the Table Window.
• The base pairs are classified into the following two categories:
  • secondary structure: defined as two or more antiparallel, consecutive, and nested (not pseudoknotted) base pairs.
  • tertiary structure: all base pairings not classifiable as secondary.
• The two categories of base pairs are shown on different background colors:
  • White: secondary structure base pairs.
  • Yellow: tertiary structure base pairs.
• For more information and detailed examples, please consult the Simple RNA Secondary and Tertiary Structure Base Pair and Unpaired Nucleotide Definitions page.

AI:

Additional Information: Indicates one or more of the following:

• B = tertiary structure: base pair.
• K = tertiary structure: pseudoknot.
• R = tertiary structure: base triple; appears as link when a base triple frequency table exists.

C:

Comparative Support Color Code. Red denotes strong support, green significant support, black weak support, and gray no support.

Help for "Base Pair Frequencies"

Aln:

Sequence Alignment ID Code. Appears on a gray background.

Explanations of Individual Codes for RNA molecules:

• 5S rRNA
• 16S rRNA
• 23S rRNA
• Group I Intron RNA
• Group IIA Intron RNA
• Group IIB Intron RNA
• tRNA

Base Pair Types:

The 5' nucleotide (with a lower position number) appears first in each pair, and the 3' nucleotide (higher position number) appears second.

Different classes of pairing appear on colored backgrounds (described below).

The frequencies appearing in these columns are calculated as:

Frequencies greater than 2% appear in bold type; values of 0.0 are shown as "--."

gap:

The percentage of sequences with deletions at one or both positions for the given base pair are shown on a cyan background.

Seq:

Number of sequences with sequence information (A, G, C, U, -) at the two base pair positions. Appears on a gray background.

Help for "Base Pair Collective Scoring Data":

This section (more detailed descriptions) is under construction.

Aln:

Sequence Alignment ID Code. Appears on a gray background.

Explanations of Individual Codes for RNA molecules:

• 5S rRNA
• 16S rRNA
• 23S rRNA
• Group I Intron RNA
• Group IIA Intron RNA
• Group IIB Intron RNA
• tRNA

Xch, Ych:

Numbers of phylogenetic changes (at positions x and y respectively). Shown on a cyan background.

PE:

Number of phylogenetic events. Shown on a cyan background.

PES:

Phylogenetic event score. Shown on a cyan background.

Cov1:

Covary1 score. Shown on a magenta background.

Cov3:

Covary3 score. Shown on a magenta background.

C1+C3:

Sum of the Covary1 and Covary3 scores. Shown on a magenta background. Primary filtering criterion for collective scoring.

WC:

Fraction of Watson-Crick (GC, CG, AU, and UA) base pairs. Shown on a yellow background. Calculated as:

WCGU:

Fraction of Watson-Crick plus Wobble (GU and UG) base pairs. Shown on a yellow background. Calculated as:

Cons:

Conservation Values (for positions x and y, respectively). Appear on a green background. Calculated as:

where P_i is the frequency of occurence of base i at a given position and P_delta is the frequency of deletions at that position.

DfDel:

Difference in amount of deletion between positions x and y. Appears on a gray background. Used as a prefilter in the collective scoring process.

PNuc:

Percentage of sequences with nucleotides at both positions x and y. Appears on a gray background. Used as a prefilter in the collective scoring process.

Seq:

Number of sequences with sequence information (A, G, C, U, -) at the two base pair positions. Appears on a gray background.