Detection of Compound Microsatellite?

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5.5 years ago

talib429 ▴ 10

The MISA microsatellite finder (Thiel et al., 2003) is a tool for finding microsatellites in nucleotide sequences. In addition to the detection of perfect microsatellites, MISA is also able to find perfect compound microsatellites that are composed multiple occurrences of more than one simple sequence motif. How can we find these Compound Microsatellites?

RNA-Seq • 1.1k views

ADD COMMENT • link 5.5 years ago by talib429 ▴ 10

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MISA is also able to find perfect compound microsatellites that are composed multiple occurrences of more than one simple sequence motif.

reads like the answer to your question.

How can we find these Compound Microsatellites?

I recommend you rephrase your question in the original post in order make clearer what you're looking for and what it is that MISA doesn't provide you. Also, you're title is very specific, I would replace SSR with microsatellite

ADD REPLY • link 5.5 years ago by Carambakaracho ★ 3.3k

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Thank you @carambakaracho for your suggestions

ADD REPLY • link 5.5 years ago by talib429 ▴ 10

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...is that all that you wanted to say? Do you need help about how to use MISA?

ADD REPLY • link 5.5 years ago by Kevin Blighe 88k

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yes I need help for using misa. All software are based on linux based and online there a limitation of 2mb for sequences to upload can you help me with misa in offline mode.

ADD REPLY • link 5.5 years ago by talib429 ▴ 10

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It sounds like you need more practical help than we can reasonably provide. For example, if you need to use linux, you could:

install a linux virtual environment on your current operating system
use the Windows 10 linux subsystem
rent some 'cloud' server space, e.g., Amazon AWS

Is there nobody locally who can help?

ADD REPLY • link 5.5 years ago by Kevin Blighe 88k

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