Bioinformatics Solutions Inc.

Answer.PatternHunter is a general purpose homology search software. It is many times faster than Blast and is more sensitive.

Answer.Current software is too slow, runs out of memory and is unreliable in many applications that compare large amounts of data.

Answer.PatternHunter uses a patented spaced seed technology and algorithm for handling hit generation, hit extension and gap extension. Every day, researchers are faced with large amounts of data and long processing times. PatternHunter determines fast and reliable answers, at high sensitivities, using little memory and a desktop computer.

4. Question:How does PatternHunter's algorithm compare with the Smith-Waterman and Needleman-Wunsch algorithms?

Answer.The Needleman-Wunsch algorithm finds the best global alignment between two sequences, whereas Smith-Waterman and PatternHunter find the best local alignments. Smith-Waterman assigns a negative score/weight to mismatches (e.g. it requires a gap penalty); this has the effect of maximizing locally optimal alignments at the expense of the global alignment. Needleman-Wunsch usually loses subsequence matches. Both Smith-Waterman and Needleman-Wunsch compare all bases in one sequence against all bases in another sequence, a time consuming method which doesn't lend itself well to large DNA sequences. PatternHunter indexes one sequence and uses this to quickly find short exact "seed" matches (hits), which are then extended into longer alignments. With the optimal multiple spaced seed technology, PatternHunter achieves Smith-Waterman sensitivity at a speed 3000 times faster. See the PatternHunter II paper for further details - this can be found in the PatternHunter papers section of the BSi website at www.bioinformaticssolutions.com.

Answer.PatternHunter has been proven to be more sensitive and is two orders of magnitude faster than BLAST when processing large sequences and requires only a fraction of the memory.

6. Question:If I know how to use Blast, is it easy for me to use PatternHunter?

Answer.Yes. PatternHunter's input commands and parameters are very similar. PatternHunter's standard output is similar to BLAST's, and can be made identical to BLAST's at the user's choice.

Answer.No. PatternHunter processes any genome on any computer, including a desktop.

9. Question:If I have a supercomputer, will I get faster results using PatternHunter?

10. Question:Exactly how fast is PatternHunter when comparing two DNA sequences?

Answer.PatternHunter was used to compare the Human Genome (3 Gbase) against 16 million reads of the Mouse Genome (3 coverage, 9 Gbase total). It took only 21 days using a Pentium 3/700 MHz desktop computer with 1G of RAM. On the same machine and at the same sensitivity, Blast would take years.

11. Question:Is there anything else that affects PatternHunter's performance?

Answer.Different Java Virtual Machines may change the performance speed of PatternHunter significantly. Some old Java VMs without JIT or HotSpot may reduce the run time speed by a factor of 10. Make sure that you have the most updated Java VM installed on your system.

Answer. Yes. PatternHunter 2.0 supports queries against (and between) databases.

13. Question:What is the largest DNA sequence comparison achieved on PatternHunter?

Answer.PatternHunter's largest sequence comparison was the human genome verses the mouse genome.

Answer.Yes. Patternhunter now gives you the ability to see your results just as you would Blast, but without the wait or using huge amounts of memory.

Answer.A free demo version of PatternHunter is available at the BSi web site http://www.bioinformaticssolutions.com/products/ph/download.php. After filling out the web form, we will email a password to you. You may then use this password to download the 30 day, limited functionality demo. Please note, demo verison is a MS Windows application which can only be used on MS Windows, whereas the full version is distributed in Jar file and can be used on any Java 2 enabled platform.

16. Question:Why does the demo verion give run time error like "Unable to start the application--the Java Virtual Machine cannot be loaded. Class not registered."

Answer.Some distributions of Windows XP do not contain java VM, which PatternHunter requires. In such cases, you need to either install SP1, or download msjavx86.exe from our the BSi website at the same place as the PatternHunter demo.

Answer.First, make sure JDK 1.4 or better is installed on your system. Currently PatternHunter can only be started from a command line, so access the command prompt through your Start Menu -> Programs -> Accessories -> command prompt. Now type java -jar PH.jar and you should see a list of available options.

Answer.Currently PatternHunter can only be started from a command line, so access the command prompt through your Start Menu -> Programs -> Accessories -> command prompt. From the directory containing ph.exe, type ph. This will tell you what options are available.

Answer.Suppose your sequences are stored in seq1.fna, seq2.fna. Type the command line:

to compare the two sequences. If you are running the PatternHunter demo version, replace "java -jar PH.jar" with "ph".

to find repeats within this sequence. If you are running the PatternHunter demo version, replace "java -jar PH.jar" with "ph".

Answer.Java is preset to use a limited amount of memory. If you get an out of memory error then you will need to tell Java to use more memory. You can tell Java to use as much memory as you have physical memory on your system. To tell java, for example, to use 256 MB of memory, type:

23. Question:Can I compare a DNA sequence to itself by using it for both the 1st and 2nd sequence?

Answer.Yes, but this is not very useful because PatternHunter will find that the whole sequence matches itself and will find every repeat twice. To compare a DNA sequence to itself, you should omit the -j argument, which forces PatternHunter to ignore the trivial match and the duplicate matches.

Answer.See BSI's list of references on the PatternHunter product information page.

	News \| Products Downloads Support User Comments Corporate
Overview Approach Product Line Benchmark Download Demo Academic Download Request Prices Tech Support User Comments	Superior homology search Software PatternHunter PatternHunter Frequently Asked Questions 1. Question: What is PatternHunter? 2. Question: Why was the PatternHunter software program developed? 3. Question:What makes PatternHunter different from existing programs? 4. Question:How does PatternHunter's algorithm compare with the Smith-Waterman and Needleman-Wunsch algorithms? 5. Question:Why use PatternHunter instead of Blast? 6. Question:If I know how to use Blast, is it easy for me to use PatternHunter? 7. Question:How big is the program? 8. Question:Do I need a powerful computer to run PatternHunter? 9. Question:If I have a supercomputer, will I get faster results using PatternHunter? 10. Question:Exactly how fast is PatternHunter when comparing two DNA sequences? 11. Question:Is there anything else that affects PatternHunter's performance? 12. Question:Can PatternHunter query a database? 13. Question:What is the largest DNA sequence comparison achieved on PatternHunter? 14. Question:Can I see my results in BLAST-style format? 15. Question:How can I evaluate PatternHunter? 16. Question:Why does the demo verion give run time error like "Unable to start the application--the Java Virtual Machine cannot be loaded. Class not registered." 17. Question:How can I get a price quote for PatternHunter? 18. Question:How do I start PatternHunter full version from Windows? 19. Question:How do I run the PatternHunter demo version? 20. Question:How do I compare two DNA sequences? 21. Question:How do I find repeats within one DNA sequence? 22. Question:I got an OutOfMemory error, how do I get around this? 23. Question:Can I compare a DNA sequence to itself by using it for both the 1st and 2nd sequence? 24. Question:Where can I find references for PatternHunter and BLAST? 1. Question: What is PatternHunter? Answer.PatternHunter is a general purpose homology search software. It is many times faster than Blast and is more sensitive. 2. Question:Why was the PatternHunter software program developed? Answer.Current software is too slow, runs out of memory and is unreliable in many applications that compare large amounts of data. 3. Question:What makes PatternHunter different from existing programs? Answer.PatternHunter uses a patented spaced seed technology and algorithm for handling hit generation, hit extension and gap extension. Every day, researchers are faced with large amounts of data and long processing times. PatternHunter determines fast and reliable answers, at high sensitivities, using little memory and a desktop computer. 4. Question:How does PatternHunter's algorithm compare with the Smith-Waterman and Needleman-Wunsch algorithms? Answer.The Needleman-Wunsch algorithm finds the best global alignment between two sequences, whereas Smith-Waterman and PatternHunter find the best local alignments. Smith-Waterman assigns a negative score/weight to mismatches (e.g. it requires a gap penalty); this has the effect of maximizing locally optimal alignments at the expense of the global alignment. Needleman-Wunsch usually loses subsequence matches. Both Smith-Waterman and Needleman-Wunsch compare all bases in one sequence against all bases in another sequence, a time consuming method which doesn't lend itself well to large DNA sequences. PatternHunter indexes one sequence and uses this to quickly find short exact "seed" matches (hits), which are then extended into longer alignments. With the optimal multiple spaced seed technology, PatternHunter achieves Smith-Waterman sensitivity at a speed 3000 times faster. See the PatternHunter II paper for further details - this can be found in the PatternHunter papers section of the BSi website at www.bioinformaticssolutions.com. 5. Question:Why use PatternHunter instead of Blast? Answer.PatternHunter has been proven to be more sensitive and is two orders of magnitude faster than BLAST when processing large sequences and requires only a fraction of the memory. 6. Question:If I know how to use Blast, is it easy for me to use PatternHunter? Answer.Yes. PatternHunter's input commands and parameters are very similar. PatternHunter's standard output is similar to BLAST's, and can be made identical to BLAST's at the user's choice. 7. Question:How big is the program? Answer.PatternHunter is less than 100Kb in a jar file. 8. Question:Do I need a powerful computer to run PatternHunter? Answer.No. PatternHunter processes any genome on any computer, including a desktop. 9. Question:If I have a supercomputer, will I get faster results using PatternHunter? Answer.Yes, definitely. 10. Question:Exactly how fast is PatternHunter when comparing two DNA sequences? Answer.PatternHunter was used to compare the Human Genome (3 Gbase) against 16 million reads of the Mouse Genome (3 coverage, 9 Gbase total). It took only 21 days using a Pentium 3/700 MHz desktop computer with 1G of RAM. On the same machine and at the same sensitivity, Blast would take years. 11. Question:Is there anything else that affects PatternHunter's performance? Answer.Different Java Virtual Machines may change the performance speed of PatternHunter significantly. Some old Java VMs without JIT or HotSpot may reduce the run time speed by a factor of 10. Make sure that you have the most updated Java VM installed on your system. 12. Question:Can PatternHunter query a database? Answer. Yes. PatternHunter 2.0 supports queries against (and between) databases. 13. Question:What is the largest DNA sequence comparison achieved on PatternHunter? Answer.PatternHunter's largest sequence comparison was the human genome verses the mouse genome. 14. Question:Can I see my results in BLAST-style format? Answer.Yes. Patternhunter now gives you the ability to see your results just as you would Blast, but without the wait or using huge amounts of memory. 15. Question:How can I evaluate PatternHunter? Answer.A free demo version of PatternHunter is available at the BSi web site http://www.bioinformaticssolutions.com/products/ph/download.php. After filling out the web form, we will email a password to you. You may then use this password to download the 30 day, limited functionality demo. Please note, demo verison is a MS Windows application which can only be used on MS Windows, whereas the full version is distributed in Jar file and can be used on any Java 2 enabled platform. 16. Question:Why does the demo verion give run time error like "Unable to start the application--the Java Virtual Machine cannot be loaded. Class not registered." Answer.Some distributions of Windows XP do not contain java VM, which PatternHunter requires. In such cases, you need to either install SP1, or download msjavx86.exe from our the BSi website at the same place as the PatternHunter demo. 17. Question:How can I get a price quote for PatternHunter? Answer.For PatternHunter pricing information, fill out the Pricing F orm. 18. Question:How do I start PatternHunter full version from Windows? Answer.First, make sure JDK 1.4 or better is installed on your system. Currently PatternHunter can only be started from a command line, so access the command prompt through your Start Menu -> Programs -> Accessories -> command prompt. Now type java -jar PH.jar and you should see a list of available options. 19. Question:How do I run the PatternHunter demo version? Answer.Currently PatternHunter can only be started from a command line, so access the command prompt through your Start Menu -> Programs -> Accessories -> command prompt. From the directory containing ph.exe, type ph. This will tell you what options are available. 20. Question:How do I compare two DNA sequences? Answer.Suppose your sequences are stored in seq1.fna, seq2.fna. Type the command line: java -jar PH.jar -i seq1.fna -j seq2.fna to compare the two sequences. If you are running the PatternHunter demo version, replace "java -jar PH.jar" with "ph". 21. Question:How do I find repeats within one DNA sequence? Answer.Suppose your sequence is stored in a file seq.fna. Then type java -jar PHD.jar -i seq.fna to find repeats within this sequence. If you are running the PatternHunter demo version, replace "java -jar PH.jar" with "ph". 22. Question:I got an OutOfMemory error, how do I get around this? Answer.Java is preset to use a limited amount of memory. If you get an out of memory error then you will need to tell Java to use more memory. You can tell Java to use as much memory as you have physical memory on your system. To tell java, for example, to use 256 MB of memory, type: java -Xmx256m -jar PH.jar -i seq.fna . 23. Question:Can I compare a DNA sequence to itself by using it for both the 1st and 2nd sequence? Answer.Yes, but this is not very useful because PatternHunter will find that the whole sequence matches itself and will find every repeat twice. To compare a DNA sequence to itself, you should omit the -j argument, which forces PatternHunter to ignore the trivial match and the duplicate matches. 24. Question:Where can I find references for PatternHunter and BLAST? Answer.See BSI's list of references on the PatternHunter product information page.