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What do the bases mean in PSAM?

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melodypluto:
Dear administrator,
I used the Convert2PSAM in order to convert the PWM into PSAM.
CODE: Convert2PSAM  -source=PW -inpfile=/mnt/tools/REDUCE-Suite-v2.2/data/formats/pwm_ex.dat -psamfile=psam=pw2psam.xml
However, there are some bases named W, instead of anyone among ACGT.
Thus I wonder the meaning of W in PSAM. Is there other type of base in PSAM? If so, what do them mean?
Could it be possible for you to show me the details about the bases in PSAM?

Thank you,
Pan Shen

xiangjun:
Dear Pan Shen,

Thanks for using the REDUCE Suite and for asking your questions on the Forum.

The W in the converted PSAM notation means A or T (Weak, since the A-T Watson-Crick pair has two H-bonds, compared to three in a G-C pair). Not surprising, S (for Strong) represents G or C.

More details on "Nucleic acid notation" can be found in the Wikipedia, among many other online resources.

Hope this helps.

Xiang-Jun

melodypluto:
Thank you very much! ;D

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