AnalyzeAlign

Purpose: Show weblogos, calculate frequency by position, and find variants in an alignment. Explanation.

Input

Alignment [Sample Input]	Paste or upload alignment       Use LANL database alignment      Alignment type Filtered web  Web  Subtype reference  Compendium       Organism HIV-1/SIVcpz  HIV-2/SIVsmm   Other SIV      Region Complete 5'LTR Gag Pol Vif Vpr Tat Rev Vpu Vpx Env Nef      Subtypes All   Major subtypes (A B C D F G CRF01 CRF02)
Sequence type	nucleotide   amino acid
Positions/range to analyze	Total positions ≤ 200!
Range numbers refer to	alignment columns, including gaps residues of 1st sequence residues of HXB2 (K03455)
Group the sequences	Report results for all sequences as a single group Report separate results for subsets of sequences (email results)        Group sequences by:      the characters in field of names delimited by   first character(s) in names   paste or upload grouped sequence names (example)             I am using a LANL alignment; group sequences by subtypes (the first field)        Combine logos into a page:           Concatenate as a x matrix      Orientation: Portrait   Landscape      Include removed logos:
Email results

 Logo options

Logo size	stack width pixels   size small medium large
Max no. of logo stacks per line
Figure title
Figure label
X-axis labels	Show   Label: Stack annotations:          (A comma separated list, must be same length as sequence range)
Y-axis units	probability bits nats kT kJ/mol kcal/mol
Y-axis label	Show   Label:
Color scheme	Select predefined scheme    Auto (NA: Base pairing, AA: Hydrophobicity) Monochrome (NA) Base pairing (NA) Classic (NA) Hydrophobicity (AA) Chemistry (AA) Charge (AA) Paste or upload custom color scheme (example)       Specify symbol colors    Symbols Color
Remove symbols from logo	consensus of alignment   consensus of seq group   residues of 1st seq of alignment   residues of 1st seq of seq group user-specified     add removed symbols to stack annotations do not remove, show all
Potential N-linked glycosylation sites	Mark  (for amino acid sequences only)

 Other options

Cut-off for calculating frequency by position	%
Master sequence for finding variants	consensus of alignment   consensus of seq group 1st seq of alignment   1st seq of seq group user-specified

Related links:

• AnalyzeAlign Explanation
• LANL alignments describes the different types of premade alignments available.
• WebLogo 3