SeqPF - Sequence Pattern Finder
SeqPF is an online tool to find conserved regions in the biological sequence by pattern matching. The allowed wildcard characters are .+*?!|^$()[]{}\
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Pattern Rules: [hide]
Character | Description | Example |
---|---|---|
* | Matches zero or more of preceding character or item range. | CAT* finds CA followed by zero or more T's. Example: CA, CAT, CATT. (CAT)* finds zero or more CAT's. Example: CAT, CATCAT. |
+ | Matches one or more of preceding character or item range. | CAT+ finds CAT followed by zero or one character. Example: CAT, CATT. (CAT)+ finds one or more CAT's. Example: CAT, CATCAT. |
. | Matches almost any single character. | CAT. finds CAT followed by one character. Example: CATA, CATT, CATC. |
? | Matches zero or one of preceding character or item range. | CAT? finds CAT followed by zero or one character. Example: CA, CAT. (CAT)? finds one or one CAT's. Example: CAT, CATCAT. |
[ ] | Matches a range of characters within the brackets. | A[TC]G finds ATC, ACG. |
( ) | Matches a group of expressions. | (AA|AT|AC|AG) finds AA, AT, AC, AG. |
[!] OR [^] | Excludes a range of characters within the brackets. | A[!TC]G finds AAC, AGG. A[^TC]G finds AAC, AGG. |
| | It is the logical OR symbol. | (AT|ATC) finds ATG, ATCG. |
- | Matches a range of characters within the brackets, used with hypen symbol. But, not in reverse order. | A[B-D]E finds ABE, ACE, ADE. |
\ | Matches word characters including all lower and upper case letters. | \w finds all characters. |
^ | Matches the start of sequence. | ^CAT finds the sequence that begins with CAT. |
$ | Matches the end of sequence. | CAT$ finds the sequence that ends with CAT. ^ATCG$ finds identical sequence matching ATCG. |
{ } | Matches exactly n times of preceding character or item range (OR) atleast n but not more than m times. | (CAT){n} finds CAT n times. (CAT){n,} finds CAT at least n times. (CAT){n,m} finds CAT at least n times but not more than m times. ((AT)[CG]{n,m} finds ATC or ATG at least n times but not more than m times. |