diff --git a/biojava-core/src/main/java/demo/ParseFastaFileDemo1.java b/biojava-core/src/main/java/demo/ParseFastaFileDemo1.java
new file mode 100755
index 0000000000..716769e7ba
--- /dev/null
+++ b/biojava-core/src/main/java/demo/ParseFastaFileDemo1.java
@@ -0,0 +1,123 @@
+/*
+ *                    BioJava development code
+ *
+ * This code may be freely distributed and modified under the
+ * terms of the GNU Lesser General Public Licence.  This should
+ * be distributed with the code.  If you do not have a copy,
+ * see:
+ *
+ *      http://www.gnu.org/copyleft/lesser.html
+ *
+ * Copyright for this code is held jointly by the individual
+ * authors.  These should be listed in @author doc comments.
+ *
+ * For more information on the BioJava project and its aims,
+ * or to join the biojava-l mailing list, visit the home page
+ * at:
+ *
+ *      http://www.biojava.org/
+ *
+ */
+package demo;
+
+
+import java.io.File;
+import java.io.InputStream;
+import java.util.LinkedHashMap;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+import org.biojava.nbio.core.sequence.ProteinSequence;
+import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
+import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
+import org.biojava.nbio.core.sequence.io.FastaReader;
+import org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser;
+import org.biojava.nbio.core.sequence.io.ProteinSequenceCreator;
+import org.biojava.nbio.core.util.InputStreamProvider;
+
+
+/**
+ * Created by andreas on 6/17/15.
+ */
+public class ParseFastaFileDemo1 {
+
+
+	public String testMethod(String a) {
+		return a + " - Teste";
+	}
+
+	/** e.g. download ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz
+	 * and pass in path to local location of file
+	 *
+	 * @param args
+	 */
+		public static void main(String[] args) {
+
+			int mb = 1024*1024;
+
+			//Getting the runtime reference from system
+			Runtime runtime = Runtime.getRuntime();
+
+			System.out.println("##### Heap utilization statistics [MB] #####");
+
+			//Print used memory
+			System.out.println("Used Memory:"
+					+ (runtime.totalMemory() - runtime.freeMemory()) / mb);
+
+			//Print free memory
+			System.out.println("Free Memory:"
+					+ runtime.freeMemory() / mb);
+
+			//Print total available memory
+			System.out.println("Total Memory:" + runtime.totalMemory() / mb);
+
+			//Print Maximum available memory
+			System.out.println("Max Memory:" + runtime.maxMemory() / mb);
+
+
+			if ( args.length < 1) {
+				System.err.println("First argument needs to be path to fasta file");
+				return;
+			}
+
+			File f = new File(args[0]);
+
+			if ( ! f.exists()) {
+				System.err.println("File does not exist " + args[0]);
+				return;
+			}
+
+			long timeS = System.currentTimeMillis();
+
+			try {
+
+				// automatically uncompress files using InputStreamProvider
+				InputStreamProvider isp = new InputStreamProvider();
+
+				InputStream inStream = isp.getInputStream(f);
+
+
+				FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>(
+						inStream,
+						new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
+						new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
+
+				LinkedHashMap<String, ProteinSequence> b;
+
+				int nrSeq = 0;
+
+				while ((b = fastaReader.process(100)) != null) {
+					for (String key : b.keySet()) {
+						nrSeq++;
+						//System.out.println(nrSeq + " : " + key + " " + b.get(key));
+						if ( nrSeq % 100000 == 0)
+							System.out.println(nrSeq );
+					}
+
+				}
+				long timeE = System.currentTimeMillis();
+				System.out.println("parsed a total of " + nrSeq + " TREMBL sequences! in " + (timeE - timeS));
+			} catch (Exception ex) {
+				Logger.getLogger(ParseFastaFileDemo.class.getName()).log(Level.SEVERE, null, ex);
+			}
+		}
+}
diff --git a/biojava-core/src/main/java/demo/ParseFastaFileDemo3.java b/biojava-core/src/main/java/demo/ParseFastaFileDemo3.java
new file mode 100755
index 0000000000..3f5bbf2e7f
--- /dev/null
+++ b/biojava-core/src/main/java/demo/ParseFastaFileDemo3.java
@@ -0,0 +1,123 @@
+/*
+ *                    BioJava development code
+ *
+ * This code may be freely distributed and modified under the
+ * terms of the GNU Lesser General Public Licence.  This should
+ * be distributed with the code.  If you do not have a copy,
+ * see:
+ *
+ *      http://www.gnu.org/copyleft/lesser.html
+ *
+ * Copyright for this code is held jointly by the individual
+ * authors.  These should be listed in @author doc comments.
+ *
+ * For more information on the BioJava project and its aims,
+ * or to join the biojava-l mailing list, visit the home page
+ * at:
+ *
+ *      http://www.biojava.org/
+ *
+ */
+package demo;
+
+
+import java.io.File;
+import java.io.InputStream;
+import java.util.LinkedHashMap;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+import org.biojava.nbio.core.sequence.ProteinSequence;
+import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
+import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
+import org.biojava.nbio.core.sequence.io.FastaReader;
+import org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser;
+import org.biojava.nbio.core.sequence.io.ProteinSequenceCreator;
+import org.biojava.nbio.core.util.InputStreamProvider;
+
+
+/**
+ * Created by andreas on 6/17/15.
+ */
+public class ParseFastaFileDemo3 {
+
+
+	public String testMethod(String a) {
+		return a + " - Teste";
+	}
+
+	/** e.g. download ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz
+	 * and pass in path to local location of file
+	 *
+	 * @param args
+	 */
+		public static void main(String[] args) {
+
+			int mb = 1024*1024;
+
+			//Getting the runtime reference from system
+			Runtime runtime = Runtime.getRuntime();
+
+			System.out.println("##### Heap utilization statistics [MB] #####");
+
+			//Print used memory
+			System.out.println("Used Memory:"
+					+ (runtime.totalMemory() - runtime.freeMemory()) / mb);
+
+			//Print free memory
+			System.out.println("Free Memory:"
+					+ runtime.freeMemory() / mb);
+
+			//Print total available memory
+			System.out.println("Total Memory:" + runtime.totalMemory() / mb);
+
+			//Print Maximum available memory
+			System.out.println("Max Memory:" + runtime.maxMemory() / mb);
+
+
+			if ( args.length < 1) {
+				System.err.println("First argument needs to be path to fasta file");
+				return;
+			}
+
+			File f = new File(args[0]);
+
+			if ( ! f.exists()) {
+				System.err.println("File does not exist " + args[0]);
+				return;
+			}
+
+			long timeS = System.currentTimeMillis();
+
+			try {
+
+				// automatically uncompress files using InputStreamProvider
+				InputStreamProvider isp = new InputStreamProvider();
+
+				InputStream inStream = isp.getInputStream(f);
+
+
+				FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>(
+						inStream,
+						new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
+						new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
+
+				LinkedHashMap<String, ProteinSequence> b;
+
+				int nrSeq = 0;
+
+				while ((b = fastaReader.process(100)) != null) {
+					for (String key : b.keySet()) {
+						nrSeq++;
+						//System.out.println(nrSeq + " : " + key + " " + b.get(key));
+						if ( nrSeq % 100000 == 0)
+							System.out.println(nrSeq );
+					}
+
+				}
+				long timeE = System.currentTimeMillis();
+				System.out.println("parsed a total of " + nrSeq + " TREMBL sequences! in " + (timeE - timeS));
+			} catch (Exception ex) {
+				Logger.getLogger(ParseFastaFileDemo.class.getName()).log(Level.SEVERE, null, ex);
+			}
+		}
+}
diff --git a/biojava-core/src/main/java/demo/ParseFastaFileDemo4.java b/biojava-core/src/main/java/demo/ParseFastaFileDemo4.java
new file mode 100755
index 0000000000..cd9614bacc
--- /dev/null
+++ b/biojava-core/src/main/java/demo/ParseFastaFileDemo4.java
@@ -0,0 +1,124 @@
+/*
+ *                    BioJava development code
+ *
+ * This code may be freely distributed and modified under the
+ * terms of the GNU Lesser General Public Licence.  This should
+ * be distributed with the code.  If you do not have a copy,
+ * see:
+ *
+ *      http://www.gnu.org/copyleft/lesser.html
+ *
+ * Copyright for this code is held jointly by the individual
+ * authors.  These should be listed in @author doc comments.
+ *
+ * For more information on the BioJava project and its aims,
+ * or to join the biojava-l mailing list, visit the home page
+ * at:
+ *
+ *      http://www.biojava.org/
+ *
+ */
+package demo;
+
+
+import java.io.File;
+import java.io.InputStream;
+import java.util.LinkedHashMap;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+import org.biojava.nbio.core.sequence.ProteinSequence;
+import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
+import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
+import org.biojava.nbio.core.sequence.io.FastaReader;
+import org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser;
+import org.biojava.nbio.core.sequence.io.ProteinSequenceCreator;
+import org.biojava.nbio.core.util.InputStreamProvider;
+
+
+/**
+ * Created by andreas on 6/17/15.
+ */
+public class ParseFastaFileDemo4 {
+
+
+	public String testMethod(String a) {
+		return a + " - Teste";
+	}
+		
+		
+	/** e.g. download ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz
+	 * and pass in path to local location of file
+	 *
+	 * @param args
+	 */
+		public static void main(String[] args) {
+
+			int mb = 1024*1024;
+
+			//Getting the runtime reference from system
+			Runtime runtime = Runtime.getRuntime();
+
+			System.out.println("##### Heap utilization statistics [MB] #####");
+
+			//Print used memory
+			System.out.println("Used Memory:"
+					+ (runtime.totalMemory() - runtime.freeMemory()) / mb);
+
+			//Print free memory
+			System.out.println("Free Memory:"
+					+ runtime.freeMemory() / mb);
+
+			//Print total available memory
+			System.out.println("Total Memory:" + runtime.totalMemory() / mb);
+
+			//Print Maximum available memory
+			System.out.println("Max Memory:" + runtime.maxMemory() / mb);
+
+
+			if ( args.length < 1) {
+				System.err.println("First argument needs to be path to fasta file");
+				return;
+			}
+
+			File f = new File(args[0]);
+
+			if ( ! f.exists()) {
+				System.err.println("File does not exist " + args[0]);
+				return;
+			}
+
+			long timeS = System.currentTimeMillis();
+
+			try {
+
+				// automatically uncompress files using InputStreamProvider
+				InputStreamProvider isp = new InputStreamProvider();
+
+				InputStream inStream = isp.getInputStream(f);
+
+
+				FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>(
+						inStream,
+						new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
+						new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
+
+				LinkedHashMap<String, ProteinSequence> b;
+
+				int nrSeq = 0;
+
+				while ((b = fastaReader.process(100)) != null) {
+					for (String key : b.keySet()) {
+						nrSeq++;
+						//System.out.println(nrSeq + " : " + key + " " + b.get(key));
+						if ( nrSeq % 100000 == 0)
+							System.out.println(nrSeq );
+					}
+
+				}
+				long timeE = System.currentTimeMillis();
+				System.out.println("parsed a total of " + nrSeq + " TREMBL sequences! in " + (timeE - timeS));
+			} catch (Exception ex) {
+				Logger.getLogger(ParseFastaFileDemo.class.getName()).log(Level.SEVERE, null, ex);
+			}
+		}
+}