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Statistics The Number Of Identical Sequence Between Different Samples And In One Sample

I have three samples,they are small RNAs and these three or more samples were sequenced by Solexa high-thoughput sequencing.They are fasta format,the length of reads are 18-28nt.I want to statistics the number of identical sequence between different samples . their names are a.fa,b.fa,c.fa, For example.

a.fa

>1×4
ATCG
>2×10
ACTG
>3×12
GAAG

b.fa

>1×13
GAAG
>2×14
 ATCG

c.fa

>1×8
ACTG
>2×5
AAG

The result is like below.

sequence a b c
ATCG     4 14 0
ACTG     10 0 8
GAAG     12 13 0
AAG      0 0 5
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written by 2011101101 • 2011101101

duplicated submission other post answered

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written by Istvan Albert Istvan Albert

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