PortEco logo

Sequence Assembly Exercise

From EcoliWiki
Jump to: navigation, search

DNA Sequence Assembly

Tools to illustrate sequence assembly

TAMU Genomics Read Maker

Converting the beginning of The Origin of Species into paired-end reads

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 Darwin):

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.

Output:

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
...