How do I search for a motif within my sequences in the Sequence Viewer?

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 "<".

Sequence searches

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 

Translation searches

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:

Annotation search

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.