diff --git a/src/org/biojavax/bio/seq/io/FastaFormat.java b/src/org/biojavax/bio/seq/io/FastaFormat.java
index 61c7776..1d1a972 100644
--- a/src/org/biojavax/bio/seq/io/FastaFormat.java
+++ b/src/org/biojavax/bio/seq/io/FastaFormat.java
@@ -77,7 +77,7 @@ public class FastaFormat extends RichSequenceFormat.HeaderlessFormat {
        protected static final Pattern dp = Pattern.compile( "^(gi\\|(\\d+)\\|)?(\\w+)\\|(\\w+?)(\\.(\\d+))?\\|(\\w+)?$");
 
        protected static final Pattern readableFiles = Pattern.compile(".*(fa|fas)$");
-       protected static final Pattern aminoAcids = Pattern.compile(".*[FLIPQE].*");
+       protected static final Pattern aminoAcids = Pattern.compile("[FLIPQE]", Pattern.CASE_INSENSITIVE);
 
        private FastaHeader header = new FastaHeader();
 
@@ -104,7 +104,7 @@ public class FastaFormat extends RichSequenceFormat.HeaderlessFormat {
        public SymbolTokenization guessSymbolTokenization(File file) throws IOException {
                BufferedReader br = new BufferedReader(new FileReader(file));
                br.readLine(); // discard first line
-               boolean aa = aminoAcids.matcher(br.readLine()).matches();
+               boolean aa = aminoAcids.matcher(br.readLine()).find();
                br.close();
                if (aa) return RichSequence.IOTools.getProteinParser();
                else return RichSequence.IOTools.getDNAParser();
@@ -134,7 +134,7 @@ public class FastaFormat extends RichSequenceFormat.HeaderlessFormat {
                stream.mark(2000); // some streams may not support this
                BufferedReader br = new BufferedReader(new InputStreamReader(stream));
                br.readLine(); // discard first line
-               boolean aa = aminoAcids.matcher(br.readLine()).matches();
+               boolean aa = aminoAcids.matcher(br.readLine()).find();
                // don't close the reader as it'll close the stream too.
                // br.close();
                stream.reset();