1，在線的CAP3，少量的序列拼接

這里提供一些EST序列，用于拼接的測試。完了后生成幾個文件。有兩個說一下，有一個是”.qual”文件, 另一下是”.con/.contigs”文件。

“.qual”：FASTA序列的測序質量評價(每個堿基，The file of quality values)。大至上是數值越大，質量越低。

“.con/.contigs”：拼接好的文件

2，下載本地使用。有用于Windons版的、Linux版的等

注，Windons版的CAP3下載后需要把cap3文件，重命名為cap3.exe

運行cmd，運行cap3.exe，就能看到該程序的詳細用法。如下面所示。

Usage: /cygdrive/d/Software/bio/Cap3Win/cap3 File_of_reads [options]

File_of_reads is a file of DNA reads in FASTA format

If the file of reads is named 'xyz',

then the file of quality values must be named 'xyz.qual',

and the file of constraints named 'xyz.con'.

Options (default values):

-a? N? specify band expansion size N > 10 (20)

-b? N? specify base quality cutoff for differences N > 15 (20)

-c? N? specify base quality cutoff for clipping N > 5 (12)

-d? N? specify max qscore sum at differences N > 20 (200)

-e? N? specify clearance between no. of diff N > 10 (30)

-f? N? specify max gap length in any overlap N > 1 (20)

-g? N? specify gap penalty factor N > 0 (6)

-h? N? specify max overhang percent length N > 2 (20)

-m? N? specify match score factor N > 0 (2)

-n? N? specify mismatch score factor N < 0 (-5)

-o? N? specify overlap length cutoff > 20 (40)

-p? N? specify overlap percent identity cutoff N > 65 (80)

-r? N? specify reverse orientation value N >= 0 (1)

-s? N? specify overlap similarity score cutoff N > 400 (900)

-t? N? specify max number of word matches N > 30 (300)

-u? N? specify min number of constraints for correction N > 0 (3)

-v? N? specify min number of constraints for linking N > 0 (2)

-w? N? specify file

總結

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