Limits...
ReAlignerV: web-based genomic alignment tool with high specificity and robustness estimated by species-specific insertion sequences.

Iwama H, Hori Y, Matsumoto K, Murao K, Ishida T - BMC Bioinformatics (2008)

Bottom Line: Alignment procedures combined with computational prediction of transcription factor binding sites (TFBSs) can narrow down key regulatory elements.ReAlignerV returns ladder-like schematic alignments that integrate predicted TFBSs and the location of TEs.It also provides pair-wise alignments in which the predicted TFBS sites and their names are shown alongside each sequence.

View Article: PubMed Central - HTML - PubMed

Affiliation: Life Science Research Center, Kagawa University, Ikenobe 1750-1, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan. iwama@med.kagawa-u.ac.jp

ABSTRACT

Background: Detecting conserved noncoding sequences (CNSs) across species highlights the functional elements. Alignment procedures combined with computational prediction of transcription factor binding sites (TFBSs) can narrow down key regulatory elements. Repeat masking processes are often performed before alignment to mask insertion sequences such as transposable elements (TEs). However, recently such TEs have been reported to influence the gene regulatory network evolution. Therefore, an alignment approach that is robust to TE insertions is meaningful for finding novel conserved TFBSs in TEs.

Results: We constructed a web server 'ReAlignerV' for complex alignment of genomic sequences. ReAlignerV returns ladder-like schematic alignments that integrate predicted TFBSs and the location of TEs. It also provides pair-wise alignments in which the predicted TFBS sites and their names are shown alongside each sequence. Furthermore, we evaluated false positive aligned sites by focusing on the species-specific TEs (SSTEs), and found that ReAlignerV has a higher specificity and robustness to insertions for sequences having more than 20% TE content, compared to LAGAN, AVID, MAVID and BLASTZ.

Conclusion: ReAlignerV can be applied successfully to TE-insertion-rich sequences without prior repeat masking, and this increases the chances of finding regulatory sequences hidden in TEs, which are important sources of the regulatory network evolution. ReAlignerV can be accessed through and downloaded from http://genet.med.kagawa-u.ac.jp/.

Show MeSH

Related in: MedlinePlus

Schematic explanation of the re-aligning processes. ReAlignerV retrieves the local alignments that are produced by bl2seq in decreasing order of the bit scores. Colored blocks represent the same-direction locally aligned portions. The number above each block indicates the order of the degree of bit score. ReAlignerV adopts blue blocks and discards red and yellow ones to construct the resultant alignment. The scheme illustrated here shows the case where the noncoding sequences immediately upstream of the start codon were used to assess the specificity and robustness to TEs for the 1,490 8-kb trio orthologs.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2267439&req=5

Figure 2: Schematic explanation of the re-aligning processes. ReAlignerV retrieves the local alignments that are produced by bl2seq in decreasing order of the bit scores. Colored blocks represent the same-direction locally aligned portions. The number above each block indicates the order of the degree of bit score. ReAlignerV adopts blue blocks and discards red and yellow ones to construct the resultant alignment. The scheme illustrated here shows the case where the noncoding sequences immediately upstream of the start codon were used to assess the specificity and robustness to TEs for the 1,490 8-kb trio orthologs.

Mentions: This web server adopts the alignment method based on REALIGNER [20,21]. In brief, this method initially searches the two input sequences for locally aligned sequences using bl2seq [22]. To align short conserved blocks in the noncoding sequences appropriately, the parameter set of bl2seq is adjusted, so that word size = 7 (default) and mismatch penalty = -2 (preset). From the resultant alignments, only the same strand hits are retrieved. In decreasing order of the bit score for each local alignment, the following two steps are repeated (see Figure 2). First, when two alignments overlap, the program removes the one with the lower bit score and retains the other. Second, when two alignments are not syntenic, the alignment with the lower bit score is removed and the other is retained. If the bit scores being compared are equal, first the longer hit-stretch and then the more downstream alignment has the higher priority.


ReAlignerV: web-based genomic alignment tool with high specificity and robustness estimated by species-specific insertion sequences.

Iwama H, Hori Y, Matsumoto K, Murao K, Ishida T - BMC Bioinformatics (2008)

Schematic explanation of the re-aligning processes. ReAlignerV retrieves the local alignments that are produced by bl2seq in decreasing order of the bit scores. Colored blocks represent the same-direction locally aligned portions. The number above each block indicates the order of the degree of bit score. ReAlignerV adopts blue blocks and discards red and yellow ones to construct the resultant alignment. The scheme illustrated here shows the case where the noncoding sequences immediately upstream of the start codon were used to assess the specificity and robustness to TEs for the 1,490 8-kb trio orthologs.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2267439&req=5

Figure 2: Schematic explanation of the re-aligning processes. ReAlignerV retrieves the local alignments that are produced by bl2seq in decreasing order of the bit scores. Colored blocks represent the same-direction locally aligned portions. The number above each block indicates the order of the degree of bit score. ReAlignerV adopts blue blocks and discards red and yellow ones to construct the resultant alignment. The scheme illustrated here shows the case where the noncoding sequences immediately upstream of the start codon were used to assess the specificity and robustness to TEs for the 1,490 8-kb trio orthologs.
Mentions: This web server adopts the alignment method based on REALIGNER [20,21]. In brief, this method initially searches the two input sequences for locally aligned sequences using bl2seq [22]. To align short conserved blocks in the noncoding sequences appropriately, the parameter set of bl2seq is adjusted, so that word size = 7 (default) and mismatch penalty = -2 (preset). From the resultant alignments, only the same strand hits are retrieved. In decreasing order of the bit score for each local alignment, the following two steps are repeated (see Figure 2). First, when two alignments overlap, the program removes the one with the lower bit score and retains the other. Second, when two alignments are not syntenic, the alignment with the lower bit score is removed and the other is retained. If the bit scores being compared are equal, first the longer hit-stretch and then the more downstream alignment has the higher priority.

Bottom Line: Alignment procedures combined with computational prediction of transcription factor binding sites (TFBSs) can narrow down key regulatory elements.ReAlignerV returns ladder-like schematic alignments that integrate predicted TFBSs and the location of TEs.It also provides pair-wise alignments in which the predicted TFBS sites and their names are shown alongside each sequence.

View Article: PubMed Central - HTML - PubMed

Affiliation: Life Science Research Center, Kagawa University, Ikenobe 1750-1, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan. iwama@med.kagawa-u.ac.jp

ABSTRACT

Background: Detecting conserved noncoding sequences (CNSs) across species highlights the functional elements. Alignment procedures combined with computational prediction of transcription factor binding sites (TFBSs) can narrow down key regulatory elements. Repeat masking processes are often performed before alignment to mask insertion sequences such as transposable elements (TEs). However, recently such TEs have been reported to influence the gene regulatory network evolution. Therefore, an alignment approach that is robust to TE insertions is meaningful for finding novel conserved TFBSs in TEs.

Results: We constructed a web server 'ReAlignerV' for complex alignment of genomic sequences. ReAlignerV returns ladder-like schematic alignments that integrate predicted TFBSs and the location of TEs. It also provides pair-wise alignments in which the predicted TFBS sites and their names are shown alongside each sequence. Furthermore, we evaluated false positive aligned sites by focusing on the species-specific TEs (SSTEs), and found that ReAlignerV has a higher specificity and robustness to insertions for sequences having more than 20% TE content, compared to LAGAN, AVID, MAVID and BLASTZ.

Conclusion: ReAlignerV can be applied successfully to TE-insertion-rich sequences without prior repeat masking, and this increases the chances of finding regulatory sequences hidden in TEs, which are important sources of the regulatory network evolution. ReAlignerV can be accessed through and downloaded from http://genet.med.kagawa-u.ac.jp/.

Show MeSH
Related in: MedlinePlus