1db5c89d97fdd3c3580c4ba9b18eba6b5029c97d
max
  Thu Sep 17 05:09:56 2026 -0700
hgSearch: highlight MANE transcript(s) in RefSeq protein-position search results, refs #38285

#Preview2 week - bugs introduced now will need a build patch to fix
A gene-symbol + codon-range search (e.g. "BRCA1 100-200") maps to every
RefSeq isoform prediction sharing that genomic footprint, which can be
dozens of near-identical NP_ accessions with no indication of which one
is the clinically-relevant MANE transcript. Cross-reference the mane
bigGenePred track by genomic overlap + protein accession and call out
the MANE Select/Plus Clinical transcript(s) in their own section above
the rest, gated behind showManeInSearch (default off) in hg.conf.

diff --git src/hg/inc/bigBedFind.h src/hg/inc/bigBedFind.h
index 8b2d076d4d0..3a6156fd46a 100644
--- src/hg/inc/bigBedFind.h
+++ src/hg/inc/bigBedFind.h
@@ -4,16 +4,34 @@
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #ifndef BIGBEDFIND_H
 #define BIGBEDFIND_H
 boolean findBigBedPosInTdb(struct cart *cart, char *db, struct trackDb *tdb, char *term, struct hgPositions *hgp, struct hgFindSpec *hfs, boolean measureTiming);
 /* Find a position in a single trackDb entry */
 
 boolean findBigBedPosInTdbList(struct cart *cart, char *db, struct trackDb *tdbList, char *term, struct hgPositions *hgp, struct hgFindSpec *hfs, boolean measureTiming);
 /* find a term in a list of tracks which may include a bigBed */ 
 
 struct trackDb *getSearchableBigBeds(struct trackDb *tdbList);
 /* Given a list of tracks, return those that are searchable */
 
 boolean isTdbSearchable(struct trackDb *tdb);
 /* Check if a single tdb is searchable */
+
+struct maneLookup *maneLookupOpen(char *db, struct trackDb **tdbList);
+/* Open the "mane" bigGenePred track for db, if it exists, for repeated calls to
+ * maneStatusForRegion.  Returns NULL if this assembly has no mane track (e.g. non-human,
+ * or hg19) -- callers should treat that as "can't tell", not an error.  tdbList is passed
+ * through to tdbForTrack, so pass a pointer already shared with other tdbForTrack calls in
+ * the same request to avoid a second trackDb load. */
+
+char *maneStatusForRegion(struct maneLookup *ml, char *chrom, int start, int end,
+                          struct slName *protAccList, char **retProtAcc);
+/* Look for a MANE transcript overlapping chrom:start-end whose NCBI protein accession
+ * (ignoring version suffix) matches one of protAccList.  Returns a cloned "MANE Select" /
+ * "MANE Plus Clinical" string, or NULL if ml is NULL or there is no match.  On a match,
+ * *retProtAcc is set to a cloned copy of the matching (versioned) NCBI protein accession,
+ * so callers can identify the single MANE transcript out of a group of merged accessions. */
+
+void maneLookupClose(struct maneLookup **pMl);
+/* Close a maneLookup opened by maneLookupOpen. */
 #endif /* BIGBEDFIND_H */