JimHu: /* TAMU Genomics Read Maker */

2010-05-22T21:38:11Z

TAMU Genomics Read Maker

← Older revision		Revision as of 21:38, 22 May 2010
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	=== TAMU Genomics Read Maker ===		=== TAMU Genomics Read Maker ===
	[[File:TAMUreadmaker.jpg\|thumb\|500px\|Converting the beginning of ''The Origin of Species'' into paired-end reads]]		[[File:TAMUreadmaker.jpg\|thumb\|500px\|Converting the beginning of ''The Origin of Species'' into paired-end reads]]
	* {http://ecoliwiki.net/tools/education/assembly.php Website]		* [http://ecoliwiki.net/tools/education/assembly.php Website]
	This is a tool written for the the undergraduate/graduate genomics class at Texas A&M. Paste in any arbitrary text and set parameters to generate fragments that students can assemble by looking for overlaps. Example:		This is a tool written for the the undergraduate/graduate genomics class at Texas A&M. Paste in any arbitrary text and set parameters to generate fragments that students can assemble by looking for overlaps. Example:

JimHu at 21:37, 22 May 2010

2010-05-22T21:37:44Z

← Older revision		Revision as of 21:37, 22 May 2010
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	DNA Sequence Assembly		DNA Sequence Assembly

			== Tools to illustrate sequence assembly ==
			=== TAMU Genomics Read Maker ===
			[[File:TAMUreadmaker.jpg\|thumb\|500px\|Converting the beginning of ''The Origin of Species'' into paired-end reads]]
			* {http://ecoliwiki.net/tools/education/assembly.php Website]
			This is a tool written for the the undergraduate/graduate genomics class at Texas A&M. Paste in any arbitrary text and set parameters to generate fragments that students can assemble by looking for overlaps. Example:

			Input text (From [http://www.literature.org/authors/darwin-charles/the-origin-of-species-6th-edition/chapter-01.html Darwin]):
			<blockquote>Causes of Variability -- Effects of Habit and the use and disuse of Parts -- Correlated Variation -- Inheritance -- Character of Domestic Varieties -- Difficulty of distinguishing between Varieties and Species -- Origin of Domestic Varieties from one or more Species -- Domestic Pigeons, their Differences and Origin -- Principles of Selection, anciently followed, their Effects -- Methodical and Unconscious Selection -- Unknown Origin of our Domestic Productions -- Circumstances favourable to Man's power of Selection.

			CAUSES OF VARIABILITY.

			When we compare the individuals of the same variety or sub-variety of our older cultivated plants and animals, one of the first points which strikes us is, that they generally differ more from each other than do the individuals of any one species or variety in a state of nature. And if we reflect on the vast diversity of the plants and animals which have been cultivated, and which have varied during all ages under the most different climates and treatment, we are driven to conclude that this great variability is due to our domestic productions having been raised under conditions of life not so uniform as, and somewhat different from, those to which the parent species had been exposed under nature. There is, also, some probability in the view propounded by Andrew Knight, that this variability may be partly connected with excess of food. It seems clear that organic beings must be exposed during several generations to new conditions to cause any great amount of variation; and that, when the organisation has once begun to vary, it generally continues varying for many generations. No case is on record of a variable organism ceasing to vary under cultivation. Our oldest cultivated plants, such as wheat, still yield new varieties: our oldest domesticated animals are still capable of rapid improvement or modification.</blockquote>
			Output:
			<pre>
			text is 1888 characters. Need 629.33333333333 for 10 X coverage
			paired end fragment length is 40

			READ:0001a parent species had been expos
			READ:0001b which the parent species had

			READ:0002a ifferences and Origin -- Princ
			READ:0002b s, their Differences and Origi

			READ:0003a ings must be exposed during se
			READ:0003b be exposed during several gene

			READ:0004a nts which strikes us is, that
			READ:0004b first points which strikes us

			READ:0005a species had been exposed unde
			READ:0005b ad been exposed under nature.

			READ:0006a record of a variable organism
			READ:0006b case is on record of a variabl

			READ:0007a n; and that, when the organisa
			READ:0007b f variation; and that, when th

			READ:0008a eings must be exposed during s
			READ:0008b be exposed during several gen

			READ:0009a ion; and that, when the organi
			READ:0009b of variation; and that, when

			READ:0010a e plants and animals which hav
			READ:0010b sity of the plants and animals

			READ:0011a n Origin of our Domestic Produ
			READ:0011b f our Domestic Productions --

			READ:0012a pecies -- Domestic Pigeons, th
			READ:0012b Domestic Pigeons, their Differ

			READ:0013a irst points which strikes us i
			READ:0013b s which strikes us is, that th

			READ:0014a Habit and the use and disuse
			READ:0014b Effects of Habit and the use a

			READ:0015a ceasing to vary under cultivat
			READ:0015b vary under cultivation. Our o

			READ:0016a ent species had been exposed u
			READ:0016b s had been exposed under natur

			READ:0017a d which have varied during all
			READ:0017b ve varied during all ages unde

			READ:0018a ldest cultivated plants, such
			READ:0018b ion. Our oldest cultivated pla

			READ:0019a ch other than do the individua
			READ:0019b re from each other than do the
			...
			</pre>

Siegele: Created page with 'DNA Sequence Assembly Category:Education'

2009-06-26T18:07:05Z

Created page with 'DNA Sequence Assembly Category:Education'

New page

DNA Sequence Assembly

[[Category:Education]]

Sequence Assembly Exercise - Revision history

JimHu: /* TAMU Genomics Read Maker */

JimHu at 21:37, 22 May 2010

Siegele: Created page with 'DNA Sequence Assembly Category:Education'