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This article is part of the supplement: Eighth International Conference on Bioinformatics (InCoB2009): Computational Biology

Open Access Proceedings

TTS Mapping: integrative WEB tool for analysis of triplex formation target DNA Sequences, G-quadruplets and non-protein coding regulatory DNA elements in the human genome

Piroon Jenjaroenpun and Vladimir A Kuznetsov*

Author Affiliations

Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, 30 Biopolis str #07-01, Singapore, 138671

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BMC Genomics 2009, 10(Suppl 3):S9  doi:10.1186/1471-2164-10-S3-S9

Published: 3 December 2009

Additional files

Additional file 1:

The distribution of the number of pTTSs duplication in the human genome. Blue dash line: the distribution of the number of pTTSs duplication of all pTTSs length. Other lines: the distributions of the number of pTTSs duplication of length 15 nt, 16 nt, 17 nt, 18 nt, and 19 nt, respectively.

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Additional file 2:

The comparison of the numbers of unique pTTSs counted within the groups of short, medium and long sequence lengths. TTSs with all observed lengths found in the TTS databases were counted. The table shows a comparison of three groups of TTS length (short pTTSs, medium pTTSs, and large pTTSs). The percentage of unique pTTS versus the total number of pTTSs found in DB was calculated.

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Additional file 3:

Mapped pTTSs found in selected region (chr8:128815498-128824855). The list of pTTSs consists of TTS IDs, descriptive information (sequence context, length, strand, percentage of guanine, number of pyrimidine insertions, and presence of tandem repeat(s) and overlapped annotation tracks.

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Additional file 4:

The mapped pTTSs found in gene region (NM_002467.3; MYC gene). The list of pTTSs consists of TTS IDs, descriptive information (sequence context, length, strand, percentage of guanine, number of pyrimidine insertions, and presence of tandem repeat(s)), a distance between a given pTTS and Transcription Start Site (TSS), a distances between pTTS and start of gene or end of gene, and TTS gene location.

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Additional file 5:

The mapped pTTS found in the region (chr3:170281981-170350216). The list of pTTSs consists of TTS IDs, descriptive information (sequence context, length, strand, percentage of guanine, number of pyrimidine insertions, and presence of tandem repeat(s) and overlapped annotation tracks.

Format: XLS Size: 31KB Download file

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Additional file 6:

The mapped pTTSs found in gene region (NM_001105078.2; EVI-1 gene). The list of pTTSs consists of TTS IDs, descriptive information (sequence context, length, strand, percentage of guanine, number of pyrimidine insertions, and presence of tandem repeat(s)), a distance between a given pTTS and Transcription Start Site (TSS), a distances between pTTS and start of gene or end of gene, and TTS gene location.

Format: XLS Size: 28KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 7:

The mapped list of pTTSs found in gene region (NM_001105077.2; EVI-1 gene). The list of pTTSs consists of TTS IDs, descriptive information (sequence context, length, strand, percentage of guanine, number of pyrimidine insertions, and presence of tandem repeat(s)), a distance between a given pTTS and Transcription Start Site (TSS), a distances between pTTS and start of gene or end of gene, and TTS gene location.

Format: XLS Size: 28KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 8:

The mapped list of pTTSs found in gene region (NM_005241.2; EVI-1 gene). The list of pTTSs consists of TTS IDs, descriptive information (sequence context, length, strand, percentage of guanine, number of pyrimidine insertions, and presence of tandem repeat(s)), a distance between a given pTTS and Transcription Start Site (TSS), a distances between pTTS and start of gene or end of gene, and TTS gene location.

Format: XLS Size: 26KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data