diff --git a/searcher/src/main.rs b/searcher/src/main.rs
index f6b8fc0..995bdbb 100644
--- a/searcher/src/main.rs
+++ b/searcher/src/main.rs
@@ -38,6 +38,58 @@ struct Cli {
     output: Option<PathBuf>,
 }
 
+fn check_compatible_downsample(
+    me: &KmerMinHash,
+    other: &KmerMinHash,
+) -> Result<(), sourmash::Error> {
+    /*
+    if self.num != other.num {
+        return Err(Error::MismatchNum {
+            n1: self.num,
+            n2: other.num,
+        }
+        .into());
+    }
+    */
+    use sourmash::Error;
+
+    if me.ksize() != other.ksize() {
+        return Err(Error::MismatchKSizes);
+    }
+    if me.hash_function() != other.hash_function() {
+        // TODO: fix this error
+        return Err(Error::MismatchDNAProt);
+    }
+    if me.max_hash() < other.max_hash() {
+        return Err(Error::MismatchScaled);
+    }
+    if me.seed() != other.seed() {
+        return Err(Error::MismatchSeed);
+    }
+    Ok(())
+}
+
+fn prepare_query(search_sig: &Signature, template: &Sketch) -> Option<KmerMinHash> {
+    let mut search_mh = None;
+    if let Some(Sketch::MinHash(mh)) = search_sig.select_sketch(template) {
+        search_mh = Some(mh.clone());
+    } else {
+        // try to find one that can be downsampled
+        if let Sketch::MinHash(template_mh) = template {
+            for sketch in search_sig.sketches() {
+                if let Sketch::MinHash(ref_mh) = sketch {
+                    if check_compatible_downsample(&ref_mh, template_mh).is_ok() {
+                        let max_hash = max_hash_for_scaled(template_mh.scaled());
+                        let mh = ref_mh.downsample_max_hash(max_hash).unwrap();
+                        return Some(mh);
+                    }
+                }
+            }
+        }
+    }
+    search_mh
+}
+
 fn search<P: AsRef<Path>>(
     querylist: P,
     siglist: P,
@@ -70,7 +122,7 @@ fn search<P: AsRef<Path>>(
 
             let mut query = None;
             for sig in &query_sig {
-                if let Some(Sketch::MinHash(mh)) = sig.select_sketch(&template) {
+                if let Some(mh) = prepare_query(sig, &template) {
                     query = Some((sig.name(), mh.clone()));
                 }
             }
@@ -125,7 +177,8 @@ fn search<P: AsRef<Path>>(
             let mut search_mh = None;
             let search_sig = &Signature::from_path(&filename)
                 .unwrap_or_else(|_| panic!("Error processing {:?}", filename))[0];
-            if let Some(Sketch::MinHash(mh)) = search_sig.select_sketch(&template) {
+
+            if let Some(mh) = prepare_query(search_sig, &template) {
                 search_mh = Some(mh);
             }
             let search_mh = search_mh.unwrap();
@@ -135,7 +188,7 @@ fn search<P: AsRef<Path>>(
 
             for (name, query) in &queries {
                 let containment =
-                    query.count_common(search_mh, false).unwrap() as f64 / query.size() as f64;
+                    query.count_common(&search_mh, false).unwrap() as f64 / query.size() as f64;
                 if containment > threshold {
                     results.push((name.clone(), match_fn.clone(), containment))
                 }
diff --git a/searcher/tests/searcher_cmd.rs b/searcher/tests/searcher_cmd.rs
index bfb54ea..fa2ea2c 100644
--- a/searcher/tests/searcher_cmd.rs
+++ b/searcher/tests/searcher_cmd.rs
@@ -34,6 +34,33 @@ fn search() -> Result<(), Box<dyn std::error::Error>> {
     Ok(())
 }
 
+#[test]
+fn search_downsample() -> Result<(), Box<dyn std::error::Error>> {
+    let mut cmd = Command::cargo_bin("searcher")?;
+
+    let mut queries = NamedTempFile::new()?;
+    writeln!(queries, "tests/data/genome-s10.fa.gz.sig")?;
+
+    let mut catalog = NamedTempFile::new()?;
+    writeln!(catalog, "tests/data/genome-s10.fa.gz.sig")?;
+    writeln!(catalog, "tests/data/genome-s11.fa.gz.sig")?;
+    writeln!(catalog, "tests/data/genome-s12.fa.gz.sig")?;
+
+    cmd.args(&["--threshold", "0"])
+        .args(&["-k", "31"])
+        .args(&["--scaled", "20000"])
+        .arg(queries.path())
+        .arg(catalog.path())
+        .assert()
+        .success()
+        .stdout(contains("query,Run,containment"))
+        .stdout(contains(
+            "../genome-s10.fa.gz','tests/data/genome-s10.fa.gz.sig',1",
+        ));
+
+    Ok(())
+}
+
 #[test]
 fn search_empty_query() -> Result<(), Box<dyn std::error::Error>> {
     let mut cmd = Command::cargo_bin("searcher")?;