X-Nico

Cofactor Genomics

Upon graduation, Dr. Glasscock pursued his doctorate in Genetics at Washington University in St. Louis where he studied under Warren Gish, Ph.D., developer of the NCBI BLAST sequence analysis program.

Warren Gish

Gish's earliest contributions to BLAST were made while working at the NCBI, starting in July 1989.

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to allow users to retrieve individual sequences in part or in whole, natively, translated or reverse-complemented, and able to dump the entire contents of a BLAST database back into human-readable FASTA format.

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This was also the first time any BLAST package introduced a new database format in a manner transparent to existing users and without abandoning support for prior formats, as a result of abstracting the database I/O functions completely separately from the data analysis functions.

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In May 1996, WU-BLAST version 2.0 with gapped alignments was publicly released in the form of a drop-in upgrade for existing users of ungapped NCBI BLAST and WU-BLAST (both at version 1.4, after having forked in 1994).

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Gish also proposed multiplexing query sequences to speed up BLAST searches by an order of magnitude or more (MPBLAST); implemented segmented sequences with internal sentinel bytes, in part to aid multiplexing with MPBLAST and in part to aid analysis of segmented query sequences from shotgun sequencing assemblies;

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The resulting search programs were significantly more sensitive, but only marginally slower than ungapped BLAST,

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The empirical use of Sum statistics in the treatment of gapped alignments was validated in collaboration with Stephen Altschul, from 1994-1995.

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As an option to WU-BLAST, Gish implemented a faster, more memory-efficient and more sensitive two-hit BLAST algorithm than is used by the NCBI software.

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to the evaluation of multiple, gapped alignment scores in all BLAST search modes.

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WU-BLAST with XDF was the first BLAST suite to support accurate, comprehensive indexed-retrieval of NCBI standard sequence identifiers,

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The NCBI Experimental BLAST Network Service, running the latest BLAST software on SMP hardware against the latest sequence databases, established the NCBI in December 1989, as a convenient, one-stop shop for sequence similarity searching.

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In 1999, Gish added support to WU-BLAST for the Extended Database Format (XDF), the first BLAST database format capable of accurately representing the entire draft sequence of the human genome in full-length chromosome sequence objects.

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Little NIH funding (average 20% FTE) was received for his WU-BLAST development, starting in November 1995, and ending shortly after the September 1997 release of the NCBI gapped BLAST (“blastall”).

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At Washington University in St. Louis, Gish developed the first practical BLAST suite of programs to combine rapid gapped sequence alignment