This article documents motif sequence searching capabilities in the IP Finder databases CAS REGISTRY, GENESEQ, PATGENE, and USGENE.
To initiate sequence code match in CAS REGISTRY, use SEARCH or S, e.g., S DSDGP/SQEP. To initiate sequence code match in GENESEQ, PATGENE and, USGENE, use RUN GETSEQ, e.g., RUN GETSEQ DSDGP/SQEP.
For more documentation on Motif sequence search capabilities, see the IP Finder help file.
CAS IP Finder Motif Symbols and Characters
| Use this symbol: | When you want to: | Examples | Sample Answers |
| ^ | Search at the beginning or the end of a sequence | => S ^MCGIL/SQSP => S VCDS^/SQSFP |
“MCGIL……” "………VCDS" |
| [ ] | Specify alternate residues | => S LGP[VL]/SQSP | LGPV LGPL |
| [-] or [~] | Exclude one or more residues |
=> S PTGK[-]/SQSP => S PTGK[~H]/SQSP |
PTGKACCD |
| {#,#} {# - #} {#} |
Repeat preceding residue(s) |
=> S G(FL)(1,3}/SQSP => S GG(FL){1-3}/SQSP => S GG(FL){3}/SQSP |
GGFL GGFLFL GGFLFLF |
| . | Specify gap(s) in the sequence |
=> S SY.RPG/SQSP => S SY...RPG/SQSP |
SYARPG SYAAARPG |
| | | Specify alternate residues |
=> S ACD|KLM/SQSP => S A(CD|KL)M/SQSP |
ACD KLM ACDM AKLM |
| ? | Repeat residue(s) zero or one time | => S FLRR(RP)?K/SQSP | FLRRK FLRRRPK |
| * | Repeat residue(s) zero or more times | => S KLK(WD)*N/SQSP | KLKN KLKWDN KLKWDWDN |
| Use this symbol: | When you want to: | Examples | Sample Answers |
| + | Repeat residue(s) one or more times |
=> S AQP+/SQSP => S (AQP)+/SQSP |
AQPP AQPPP AQPPPP AQPAQP AQPAQPAQP AQPAQPAQPAQP |
| & | Join multiple sequence fragments represented as L#’s together as one (note: CAS Registry only) |
=> S KLKWD/SQSP => S ..KRYG/SQSP => S L1 & L2/SQSP |
KLKWDKRYG KLKWNQDKRYG |
CAS IP Finder Sequence Code Match Types
| Search Type | Amino Acids | Nucleic Acids | Examples |
| EXACT | /SQEP | /SQEN | => S DSDGP/SQEP => S GGAATT/SQEN |
| EXACT | /SQEFP | ---------- | => S DSDGP/SQEFP |
| SUBSEQUENCE | /SQSP | /SQSN | => S DSDGP/SQSP => S GGAATT/SQSN |
| SUBSEQUENCE FAMILY | /SQSFP | ---------- | => S DSDGP/SQSF |
CAS IP Finder Amino Acid Family Substitution Definitions
In CAS Registry, GENESEQ, PATGENE, and USGENE searches in the Subsequence Family Search of Proteins (/SQSFP) retrieve exact sequences, subsequences, and answers in which family-equivalent substitution of the query amino acids occurs. For example, the query ADHIFC/SQSFP retrieves the equivalent fragment “PQKLYC”. The table below documents the family-equivalent amino acids.
| Groups | Amino Acids |
| Neutral Weak Hydrophobic | Alanine (Ala, A) Glycine (Gly, G) Proline (Pro, P) Serine (Ser, S) Threonine (Thr, T) |
| Acid-Amines Hydrophilic | Aspartic Acid (Asp, D) Asparagine (Asn, N) Glutamic Acid (Glu, E) Glutamine (Gln, Q) |
| Basic Hydrophobic | Arginine (Arg, R) Histidine (His, H) Lysine (Lys, K) |
| Hydrophobic | Isoleucine (Ile, I) Leucine (Leu, L) Methionine (Met, M) Valine (Val, V) |
| Aromatics | Phenylalanine (Phe, F) Tryptophan (Trp, W) Tyrosine (Tyr,Y) |
| Cross Linking | Cysteine (Cys, C) |