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Arpith Chacko Jacob<br /> <b>Warning</b>: date() [<a href='function.date'>function.date</a>]: It is not safe to rely on the system's timezone settings. You are *required* to use the date.timezone setting or the date_default_timezone_set() function. In case you used any of those methods and you are still getting this warning, you most likely misspelled the timezone identifier. We selected 'America/New_York' for 'EDT/-4.0/DST' instead in <b>/home/web/arpith/b2evocore/_functions_cats.php</b> on line <b>401</b><br /> - Whole Genome Comparison using Commodity Workstations
Arpith Chacko Jacob - since 1982...

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Warning: date() [function.date]: It is not safe to rely on the system's timezone settings. You are *required* to use the date.timezone setting or the date_default_timezone_set() function. In case you used any of those methods and you are still getting this warning, you most likely misspelled the timezone identifier. We selected 'America/New_York' for 'EDT/-4.0/DST' instead in /home/web/arpith/b2evocore/_functions.php on line 359

Warning: date() [function.date]: It is not safe to rely on the system's timezone settings. You are *required* to use the date.timezone setting or the date_default_timezone_set() function. In case you used any of those methods and you are still getting this warning, you most likely misspelled the timezone identifier. We selected 'America/New_York' for 'EDT/-4.0/DST' instead in /home/web/arpith/b2evocore/_functions.php on line 391

Warning: mktime() [function.mktime]: It is not safe to rely on the system's timezone settings. You are *required* to use the date.timezone setting or the date_default_timezone_set() function. In case you used any of those methods and you are still getting this warning, you most likely misspelled the timezone identifier. We selected 'America/New_York' for 'EDT/-4.0/DST' instead in /home/web/arpith/b2evocore/_functions.php on line 342

Warning: date() [function.date]: It is not safe to rely on the system's timezone settings. You are *required* to use the date.timezone setting or the date_default_timezone_set() function. In case you used any of those methods and you are still getting this warning, you most likely misspelled the timezone identifier. We selected 'America/New_York' for 'EDT/-4.0/DST' instead in /home/web/arpith/b2evocore/_functions.php on line 358

Warning: date() [function.date]: It is not safe to rely on the system's timezone settings. You are *required* to use the date.timezone setting or the date_default_timezone_set() function. In case you used any of those methods and you are still getting this warning, you most likely misspelled the timezone identifier. We selected 'America/New_York' for 'EDT/-4.0/DST' instead in /home/web/arpith/b2evocore/_functions.php on line 359

Warning: date() [function.date]: It is not safe to rely on the system's timezone settings. You are *required* to use the date.timezone setting or the date_default_timezone_set() function. In case you used any of those methods and you are still getting this warning, you most likely misspelled the timezone identifier. We selected 'America/New_York' for 'EDT/-4.0/DST' instead in /home/web/arpith/b2evocore/_functions.php on line 391

  Whole Genome Comparison using Commodity Workstations


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Warning: date() [function.date]: It is not safe to rely on the system's timezone settings. You are *required* to use the date.timezone setting or the date_default_timezone_set() function. In case you used any of those methods and you are still getting this warning, you most likely misspelled the timezone identifier. We selected 'America/New_York' for 'EDT/-4.0/DST' instead in /home/web/arpith/b2evocore/_functions.php on line 391
Saturday 31st 2004f July 2004,
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Warning: date() [function.date]: It is not safe to rely on the system's timezone settings. You are *required* to use the date.timezone setting or the date_default_timezone_set() function. In case you used any of those methods and you are still getting this warning, you most likely misspelled the timezone identifier. We selected 'America/New_York' for 'EDT/-4.0/DST' instead in /home/web/arpith/b2evocore/_functions.php on line 358

Warning: date() [function.date]: It is not safe to rely on the system's timezone settings. You are *required* to use the date.timezone setting or the date_default_timezone_set() function. In case you used any of those methods and you are still getting this warning, you most likely misspelled the timezone identifier. We selected 'America/New_York' for 'EDT/-4.0/DST' instead in /home/web/arpith/b2evocore/_functions.php on line 359

Warning: date() [function.date]: It is not safe to rely on the system's timezone settings. You are *required* to use the date.timezone setting or the date_default_timezone_set() function. In case you used any of those methods and you are still getting this warning, you most likely misspelled the timezone identifier. We selected 'America/New_York' for 'EDT/-4.0/DST' instead in /home/web/arpith/b2evocore/_functions.php on line 391
09:56:37 pm. Posted in: Papers. 182 words.  

"Whole Genome Comparison using Commodity Workstations," Arpith Chacko Jacob, Sugata Sanyal, 2003.

http://www.arpith.com/media/papers/jacob03pdsw.pdf

Abstract— Whole genome comparison consists of comparing or aligning two genome sequences in the hope that analogous functional or physical characteristics may be observed. Sequence comparison is done via a number of slow rigorous algorithms, or faster heuristic approaches. However, due to the large size of genomic sequences, the capacity of current software is limited. In this work, we design a parallel-distributed system for the Smith-Waterman dynamic programming sequence comparison algorithm. We use subword parallelism to speedup sequence to sequence comparison using Streaming SIMD Extensions (SSE) on Intel Pentium processors. We compare two approaches, one requiring explicit data dependency handling and the other built to automatically handle dependencies. We achieve a speedup of 10 - 30 and establish the optimum conditions for each approach. We then implement a scalable and fault-tolerant distributed version of the genome comparison process on a network of workstations based on a static work allocation algorithm. We achieve speeds upwards of 8000 MCUPS on 64 workstations, one of the fastest implementations of the Smith-Waterman algorithm.