Open Access Highly Accessed Methodology article

POLYAR, a new computer program for prediction of poly(A) sites in human sequences

Malik Nadeem Akhtar1, Syed Abbas Bukhari1, Zeeshan Fazal1, Raheel Qamar12 and Ilham A Shahmuradov3*

Author Affiliations

1 Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan

2 Shifa College of Medicine, Islamabad, Pakistan

3 Department of Fundamental problems of biological productivity, Institute of Botany, Baku, Azerbaijan

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BMC Genomics 2010, 11:646  doi:10.1186/1471-2164-11-646

Published: 19 November 2010

Additional files

Additional file 1:

Supplemental Table 1 - Mahalonobis distance (D2; 38) showing the power of recognition of Upstream Pentamer Composition characteristics in different upstream regions of PAS-strong, PAS-weak and PAS-less sites.

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Additional file 2:

Supplemental Table 2 - Mahalonobis distance (D2; 38) showing the power of recognition of Downstream Pentamer Composition characteristic in different downstream regions of PAS-weak and PAS-less sites.

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Additional file 3:

Supplemental Table 3 - Nucleotide Frequency Matrices for cleavage site (+1) in PAS-strong, PAS-weak and PAS-less poly(A) sequences.

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Additional file 4:

Supplemental Table 4 - Upstream pentamers available in 20% or more of the positive set of PAS-strong sequences.

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Additional file 5:

Supplemental Table 5 - Pentamers available in 20% or more of the positive set of PAS-weak sequences.

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Additional file 6:

Supplemental Table 6 - Pentamers available in 20% or more of the positive set of PAS-less sequences.

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Additional file 7:

Supplemental Table 7 - CPU time comparison of POLYAR and polya_svm programs on 8261 poly(A) site and 19600 intronic sequences.

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Additional file 8:

Supplemental Table 8 - Comparative testing results of POLYAR, polya_svm and polyadq programs on 3748 5'-UTR sequences.

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Additional file 9:

Supplemental Table 9 - Comparative testing results of POLYAR, polya_svm and polyadq programs on 8261 randomized poly(A) site regions.

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Open Data