The Find option in the Sequence Viewer allows you to search for a motif of interest in your sequences, annotations or alignment.
To search for a motif, enter the motif of interest into the Find text box and hit enter or "". Sequence viewer will search through the all the selected sequences for that particular motif and highlights the first motif found. Hit enter or "" to move onto the second motif. You can also move back to the previous found motif by hitting Shift and Enter or "<></>".
Single residue searches matches residues exactly including ambiguous residues. For example, A matches A only and N matches N only.
A matches ATGNG
N matches ATGNG
However, motif searches consisting of ambiguous residues matches ambiguously. For example, when N is included in a motif search, N matches any residues, including other ambiguous residues and gaps.
ATGNG matches ATG[A/C/G/T]G and ATG[Y/R/W/S/K/M/D/V/H/B]G and ATG-G
ATGYG matches ATG[C/T]G and ATG[Y]G
Gaps in sequences are ignored but gaps in queries are matched.
ACGT matches CTCAC--GTRGAG
AC--GT matches CTCAC--GTRGAG, but not CTCACGTRGAG
“Greedy” matches are preferred whereby the longest match from the start point is returned.
ACNNNT matches CTCAC--GTCTRGAG, instead of CTCAC--GTCTRGAG
Like sequence search, single residue match exactly and sequences containing ambiguous residues match ambiguously.
M matches MDSLY
MDX matches MDSLY
When translation by selection and annotation (default) is selected, CDS and ORF annotations are searched. In the example below, a search for SS matches FSSY from positions 88-93 inline with the frame of the CDS annotation.
When translation by frame(s) is selected, only the currently selected frame(s) are searched. In the example below, a search for SS matches RSSC from positions 5-10 in Frame 2.
Gaps in sequences are ignored, even if they split codons. In the example below, a search for GSI matches MGSIM as translated from ATGGGTA----GTATTATG:
Searching for keywords checks each annotation’s name, type and qualifiers. An annotation must have all the keywords to match the search.
CDR matches C[A/G/T][A/G] and annotations of Type:CDR
To make the search more specific, include the annotation name and value. In the example below, a search for Name:CDR3 matches annotation with the name of CDR3 only.