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Those sequences were aligned using the global pair algorithm of MAFFT [45] which aligns large sets of distantly related sequences of similar length with high accuracy.
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Two protein sequences of each gene pair were aligned using the global sequence alignment program NEEDLE in the EMBOSS package [ 38].
The pairs were aligned using the global version of Smith-Waterman algorithm with the substitution weight matrix PAM250 and gap-open and gap-extension penalties GOP = 14, GEP = 2.
This option should be used only for short input sequences as the base pairing probabilities are calculated here using the global folding method RNAfold.
Pair-wise cDNA and protein comparisons used the global alignment program ALIGN, available at EBI, to calculate a percent identity and similarity.
FUGUE uses the global-local algorithm to align a sequence-structure pair when they greatly differ in length and uses the global algorithm in other cases.
FUGUE uses the global-local algorithm to align a sequence-structure pair when they greatly differ in length and otherwise uses the global algorithm.
First, our pipeline automatically aligned optical maps against a SwaI restriction map created in silico from the human genome reference sequence (NCBI build 35) via SOMA (Software for Optical Map Alignment) using gapped global pair wise alignment [ 56, 67].
Stereo matching was performed on the rectified cylinder stereo image pairs using the semi-global matching algorithm [21], and the matching results are shown in Fig. 12.
The two thousand base pairs upstream of predicted NBPFs in eight mammalian genomes were extracted and then aligned using the VISTA global alignment tool (Frazer et al. 2004).
For each human-rat orthologous gene pair in Ensembl (version 39), 20 kb flanks of the genomic sequence from −10 kb to +10 kb from TSSs in either species were aligned using the AVID global alignment algorithm.
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