On the blog well be publishing indepth information about ucsc genome browser features, tools, projects and related topics that we hope people will find both useful and interesting. Paste in a query sequence to find its location in the the genome. Kent was born in hawaii and grew up in san francisco, california, united states computer animation. Before becoming a bioinformatician i got a phd in biology working with with the zahler lab. Jim kents web page im a research scientist at ucsc. We provide scientists with tools to analyze the human genome, particularly, blat the. James kent 2002 blat the blastlike alignment tool, genome res 12.
Multiple sequences may be searched if separated by lines starting with followed by the sequence name. It is designed to quickly find sequences of 95% and greater similarity of length 40 bases or more. Oct 01, 2017 view jim kents profile on linkedin, the worlds largest professional community. To compile the source code, simply enter the source code directory in terminal and issue the make command. As a workaround, we suggest dividing large reference databases into multiple files. On dna queries, blat is designed to quickly find sequences with 95% or greater similarity of length 25 bases or more. Then you can select how youd like the data to be displayed. As a graduate student at the university of california santa cruz, jim kent made national headlines in june, 2000 when he performed the public project human genome assembly hours ahead of celera, helping to keep our collective dna out of. The ucsc genome browser database pubmed central pmc. Nonexclusive commercial licenses are also available. We thank jim kent and the genome bioinformatics group of. For the computation of initial proteindna spliced alignments, scipio utilizes the program blat written by jim kent.
The ones marked may be different from the article in the profile. Two papers by jim kent published in genome research jack. This would be a good chance to get your feet wet and polish your unix skills. Blat blastlike alignment tool is a pairwise sequence alignment algorithm that was developed by jim kent at the university of california santa cruz ucsc in the early 2000s to assist in the assembly and annotation of the human genome. Like most of jims software, interactive use on this web server is free to all. We just published our inaugural post written by jim kent, the ucsc genome browser. He has been a contributor to genome database projects and the 2003 winner of the benjamin franklin award early life. Bornfebruary 10 1960 19600210 age 52hawaiinationalityunited stateseducationuniversity of california, my watch list.
If this is not possible, the only alternative is to download the executables of blat and the. See downloading blat source and documentation for more information. Whilst the great majority of the jim kent series would appear to be war novels, a small handful of other purely adult or romance titles were also published in the series. This is useful when you blat a big query file to a huge reference like human whole genome sequence. The new algorithm is called blat, which is short for blast like alignment tool. The program rapidly scans for relatively short matches hits, and extends these into highscoring pairs hsps. Jim kent on life after saving the human genome project.
Blat search genome university of southern california. Before that i wrote computer art and animation programs. You can expand to see all the tracks available for the neandertal genome. The first discusses the technical aspects and optimization of kent s sequence alignment tool, blat. William james kent born february 10, 1960 is an american research scientist and computer programmer. Jim kent is known for a number of things in the bioinformatics world, including his work on the university of california santa cruz golden path genome browser and the development of the blat blastlike alignment tool rapid alignment algorithm. Ucsc genome browser bioinformatics database and software. Dna blat works by keeping an index of the entire genome in memory. He holds a bfa in dance from cornish college of the arts and has performed in seattle for the last 12 years, working and touring with scottpowell performance, mark haim, zoe.
We have found that the blat mapper by jim kent is an excellent, fast, and efficient tool for aligning reads against a divergent reference. Blat is a legacy tool for sequence alignment that is not under active development. Have you tried taking a sequence from human genome and testing it against that. He has been a contributor to genome database projects and the 2003 winner of the benjamin franklin award. Ucsc genome browser and associated tools briefings in. Blat has special code to handle introns in rnadna alignments. Sources and executables to run batch jobs on your own server are available free for academic, personal, and nonprofit purposes. Blat is a dnaprotein sequence analysis program written by jim kent at ucsc.
Kent began his programming career in 1983 with island graphics inc. Since joining thornton tomasetti in 2007, he has applied his passion for making technical subjects accessible and engaging as the firm has grown into an industry leader. Like most of jim s software, interactive use on this web server is free to all. After gigassembler, kent went on to write blat blastlike alignment tool. Join facebook to connect with jim kent and others you may know. Blat on dna is designed to quickly find sequences of 95% and greater similarity of length 40 bases or more. Ucsc generates several annotations based on mrna alignments. Parse blat result to get locations of exon and intron. Now lets look at a very useful software tool, blat, developed by jim kent at the ucsc genome bioinformatics group. Ppt distribution of introns among full length cdna. Jim kent browser concept, blat, team leader, pi bob kuhn associate director, outreach copi donna karolchik, ann zweig project management qa, docs, support katrina learned pauline fujita luvina guruvadoo steve heitner brian lee jonathan caspar matt speir sysadmins jorge garcia erich weiler gary moro. It will find perfect sequence matches of 33 bases, and sometimes find them down to 22 bases.
Jim kent business development manager caloris engineering. You can use jim kent s blat in addition toinstead of blast which can be very fast for identifying closely related sequences. It may miss more divergent or shorter sequence alignments. Blat s speed stems from an index of all nonoverlapping kmers in the genome. Do you get a different number if you increase the tile size tilesize20. I work primarily on web tools to help understand the human genome.
The output of blat is then further processed and reformatted by the following steps. Dancers jim kent hehimhis jim kent is originally from minnesota and hawaii. After gigassembler, kent went on to write blat blastlike alignment tool and the ucsc genome browser to help analyze important genome data. While all of kents genomics software is open source in the sense that the source code can be downloaded and read for free, and all of the software. Jim kent s web page im a research scientist at ucsc. William james kent born february 10, 1960 is an american research scientist and computer. Jim kent phone, address, background info whitepages. It was developed to assist in the annotation of the human genome sequence. The new algorithm is called blat, which is short for blastlike alignment tool.
In 2000, while a phd student at the university of california santa cruz, kent wrote the software which allowed the publicly funded human genome project to win the race to assemble and publish the human genome sequence. The cow sequence data may be freely downloaded, used in analyses, and repackaged in databases if the provider is properly acknowledged. It can reduce run time linearly, and use almost equal memory as the original blat program. Like most of jim s software interactive use on this web server is free to all. All files are ed, but license is hereby granted for. Kent began his programming career in 1983 with island graphics. Several billion bases of dna in a text file are difficult to interpret, however, and specialized visualization. Protein blat works in a similar manner, except with 4mers rather than 11mers. Todays exercise involves gene prediction we will use chris burges genscan to search for gene sequence among three short human chromosomal sequences.
Blat the blastlike alignment tool is a software program developed by jim kent at ucsc to identify similarities between dna sequences and protein sequences. Blat can find the genomic locations of the gene or protein sequences that you input. This directory contains genome browser and blat application binaries built for. Blat does not try to align codons that are split by introns. The protein index takes a little more than 2 gigabytes. We just published our inaugural post written by jim kent, the ucsc genome browser architect and pi, on the 2014 ebola epidemic. Considering jim kent is author of blat and how long blat has been around it seems very unlikely that you are running into some odd bug in blat. It was designed primarily to decrease the time needed to align millions of mouse genomic reads and expressed sequence tags against the human genome sequence. For the more casual blat user, check out the documentation at the ucsc web site for a little more detail about the way blat works, without tremendous amounts of mathematical equations. If you have unix skills to get started then by all means find a local computer resource or even a desktop with respectable spces. When the compiling finished, the executable pblatcluster will locate in the same directory. Blat blastlike alignment tool is a pairwise sequence alignment algorithm that was developed by jim kent at the university of.
Blat and associated genomic finding software is courtesy of jim kent see. Unfortunately, blat has a bug which causes it to crash with large reference databases, like nr see the blat wiki page. Also, we will use jim kent s blat to map our sequences back to the ucsc genome browser. This cited by count includes citations to the following articles in scholar. Whitepages people search is the most trusted directory. Jim kent on the ucsc genome browser david haussler, professor of biomolecular engineering bioinformatics expert jim kent photo by carolyn lagattuta jim kent in his garage office ca. Jim kent and david haussler at the university of california, santa cruz played a significant role in the first release of a draft human genome sequence in 2000 9, 10, which became available from ucsc by bulk download at that time. Kent continues to work at ucsc primarily on web tools to help understand the human genome. Radio, free speech radio news, high plains news service. The data is filtered based on percentage identity and near best in genome to select only those. In practice dna blat works well on primates, and protein blat on land vertebrates. Mysql databases and ancillary large data files in gbdb via an rsync download server.
Dec 19, 2001 the new algorithm is called blat, which is short for blastlike alignment tool. You can hear animals blat in the meadows the meadows. However, blat differs from blast in some significant ways. This program combined polygon tweening in 3d with simple 2d celbased animation. Heather trumbower, jim kent, hiram clawson, angie hinrichs, brian raney, mark diekhans, robert kuhn, ali sultanqurraie and donna karolchik. Jim kent is a research scientist and computer programmer best known for his work on the human genome project. For a more detailed description of the algorithm, you can see the publication by jim kent that describes blat in more detail. As a graduate student at the university of california santa cruz, jim kent made national headlines in june, 2000 when he performed the public project human genome assembly hours ahead of celera, helping to keep our collective dna out of patent disputes for years to come. Unfortunately it doesnt natively support the fastq format which is the standard output of most hts platforms. The mrna and est sequences are extracted from genbank, and are aligned against the genome using the blastlike alignment tool blat, a fast sequence alignment tool developed by jim kent.
We provide scientists with tools to analyze the human genome, particularly, blat the blastlike alignment tool. Jim kent has more than 25 years of experience in marketing and communications for scientific and technical organizations in the u. New users should consider using razers3 this is a fork of the blat package v35 written by jim kent. Facebook gives people the power to share and makes the world more open and connected. For more information on blat s internal scoring schemes and its overall nmer alignment seed strategy, refer to w. Entitled, blat the blastlike alignment tool, it can be found in genome research, april 2002. View phone numbers, addresses, public records, background check reports and possible arrest records for jim kent. The program is based on the original blat program which was written by jim kent. The software can be downloaded from the source and executable links at. Metabin uses jim kent s blat application as an alignment method that is much faster than blastx. Jim kent, a research scientist at ucsc, has published two papers in genome research.
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