Sequence Handling

Feature documentation: Sequence Handling

PrimerLab v0.1.6 introduces enhanced sequence handling for real-world genomic data.

IUPAC Ambiguous Codes

IUPAC ambiguous nucleotide codes are automatically detected and handled:

Code	Meaning	Bases
R	puRine	A or G
Y	pYrimidine	C or T
W	Weak	A or T
S	Strong	G or C
K	Keto	G or T
M	aMino	A or C
B	not A	C, G, or T
D	not C	A, G, or T
H	not G	A, C, or T
V	not T	A, C, or G

Behavior

When IUPAC codes are detected:

1. Warning displayed to user
2. Codes converted to N (masked)
3. Regions excluded from primer placement

$ primerlab stats sequence_with_iupac.fasta

📊 Sequence Statistics: TEST_IUPAC
=============================================
  Length:      500 bp
  GC Content:  48.20%
  ⚠️  IUPAC codes: ['R', 'Y'] (6 bp)
      → Will be converted to N during design
=============================================

RNA Sequences

RNA sequences (containing Uracil) are automatically detected and converted:

Detected	Converted To
U (Uracil)	T (Thymine)
u (lowercase)	t (then uppercase)

Behavior

When RNA is detected:

1. Warning displayed to user
2. U → T conversion applied
3. Design proceeds with DNA sequence

$ primerlab stats rna_sequence.fasta

📊 Sequence Statistics: TEST_RNA
=============================================
  Length:      300 bp
  ⚠️  RNA detected (contains U)
      → Will be converted to T during design
=============================================

Sequence Validation

PrimerLab validates sequences before design:

Check	Requirement	Error Code
Length	≥ 50 bp	ERR_SEQ_TOO_SHORT
Characters	A, T, G, C, N only	ERR_SEQ_INVALID_CHAR
Non-empty	Sequence provided	ERR_SEQ_EMPTY

Use primerlab stats

Always check your sequence before design:

primerlab stats input.fasta