PeptideMapper for Multiple Sequences

Accepts .fasta, .fas, .fa, .txt files. Multiple sequences supported for comparative analysis.

Preset Rules:

Show annotations for all peptides (ignore mass filter)

Apply Rules Clear Rules

Format: [S#:]Identifier shape color[opacity] [placement] [direction] [level]

Multi-Sequence Support:
• K fill red - Apply to all sequences
• S1:K fill red - Apply only to sequence 1
• S2:P4 text "Mutant" red out above - Apply only to sequence 2

Identifiers:
• Amino acid letter (K, R, C, etc.)
• Position number (121, 45, etc.)
• Peptide number (P1, P4, P10, etc.)

Shapes:
• fill - Colors entire peptide
• circle - Circle marker
• square - Square marker
• diamond - Diamond shape marker
• text - Text label (see below)

Text Content (for text shape):
• sequence - Shows peptide sequence
• mass - Shows mass in Da
• mh - Shows [M+H]+ mass with "+" suffix
• m2h - Shows [M+2H]++ mass with "++" suffix
• "Custom text" - Any text in quotes

Colors with Transparency:
red, green, blue, magenta, cyan, yellow, orange, purple, white, black
• red - 100% opacity (solid)
• red50 - 50% opacity (semi-transparent)
• blue25 - 25% opacity (mostly transparent)

Placement (Multi-sequence only supports 'in'):
• in - Inside peptide rectangle (automatic for stacked maps)
• out - External with connecting line (single sequence only)

Direction (for 'out' only):
• above - Above the peptide
• below - Below the peptide (default)

Levels (for text 'out' only):
• L1 - Closest to peptide (default)
• L2 - Medium distance
• L3 - Furthest from peptide

Examples (auto-converted to 'in' for stacked maps):
K fill red - Red peptides containing K (all sequences)
S1:C circle yellow - Yellow dots on cysteines in sequence 1
S2:P4 text "Mutation" red - Label mutation in sequence 2
P5 text mass blue - Show mass in all sequences
S1:121 text "WT" green - Mark wild-type position
S2:121 text "Mutant" red - Mark mutant position

Multi-sequence comparison example:
S1:P4 text "Wild-type" green out above L1
S2:P4 text "Mutant" red out above L1
S1:C fill green50
S2:C fill red50