| Input: nucleotide profiles |${P}_1\ \mathrm{and}\ {P}_2$| Output: aligned profiles |${P}_{a1}\ \mathrm{and}\ {P}_{a2}$| Assume |$len\left({P}_1\right)\ge len\left({P}_2\right)$| 1. Simplify |${P}_1\ \mathrm{and}\ {P}_2$| as two modified consensus sequences |${S}_1\ \mathrm{and}\ {S}_2$|. 2. Build the FM-index for |${S}_1$|. 3. While |$i< len\left({S}_2\right)$|, |$i$| starts at 1. Begin index |$i$| in |${S}_2$| to find the longest common substrings |$lc{s}_j$| in |${S}_1$|. i + = len(lcsj) 4. The selection of optimized longest and non-overlapped common substring combinations. 5. Directly align the profile region relative to the optimized common substrings, and use k-banded DP to align the remaining profile segments individually. Join all aligned segments together to return the aligned profiles |${P}_{a1}\ \mathrm{and}\ {P}_{a2}$| |
| Input: nucleotide profiles |${P}_1\ \mathrm{and}\ {P}_2$| Output: aligned profiles |${P}_{a1}\ \mathrm{and}\ {P}_{a2}$| Assume |$len\left({P}_1\right)\ge len\left({P}_2\right)$| 1. Simplify |${P}_1\ \mathrm{and}\ {P}_2$| as two modified consensus sequences |${S}_1\ \mathrm{and}\ {S}_2$|. 2. Build the FM-index for |${S}_1$|. 3. While |$i< len\left({S}_2\right)$|, |$i$| starts at 1. Begin index |$i$| in |${S}_2$| to find the longest common substrings |$lc{s}_j$| in |${S}_1$|. i + = len(lcsj) 4. The selection of optimized longest and non-overlapped common substring combinations. 5. Directly align the profile region relative to the optimized common substrings, and use k-banded DP to align the remaining profile segments individually. Join all aligned segments together to return the aligned profiles |${P}_{a1}\ \mathrm{and}\ {P}_{a2}$| |
| Input: nucleotide profiles |${P}_1\ \mathrm{and}\ {P}_2$| Output: aligned profiles |${P}_{a1}\ \mathrm{and}\ {P}_{a2}$| Assume |$len\left({P}_1\right)\ge len\left({P}_2\right)$| 1. Simplify |${P}_1\ \mathrm{and}\ {P}_2$| as two modified consensus sequences |${S}_1\ \mathrm{and}\ {S}_2$|. 2. Build the FM-index for |${S}_1$|. 3. While |$i< len\left({S}_2\right)$|, |$i$| starts at 1. Begin index |$i$| in |${S}_2$| to find the longest common substrings |$lc{s}_j$| in |${S}_1$|. i + = len(lcsj) 4. The selection of optimized longest and non-overlapped common substring combinations. 5. Directly align the profile region relative to the optimized common substrings, and use k-banded DP to align the remaining profile segments individually. Join all aligned segments together to return the aligned profiles |${P}_{a1}\ \mathrm{and}\ {P}_{a2}$| |
| Input: nucleotide profiles |${P}_1\ \mathrm{and}\ {P}_2$| Output: aligned profiles |${P}_{a1}\ \mathrm{and}\ {P}_{a2}$| Assume |$len\left({P}_1\right)\ge len\left({P}_2\right)$| 1. Simplify |${P}_1\ \mathrm{and}\ {P}_2$| as two modified consensus sequences |${S}_1\ \mathrm{and}\ {S}_2$|. 2. Build the FM-index for |${S}_1$|. 3. While |$i< len\left({S}_2\right)$|, |$i$| starts at 1. Begin index |$i$| in |${S}_2$| to find the longest common substrings |$lc{s}_j$| in |${S}_1$|. i + = len(lcsj) 4. The selection of optimized longest and non-overlapped common substring combinations. 5. Directly align the profile region relative to the optimized common substrings, and use k-banded DP to align the remaining profile segments individually. Join all aligned segments together to return the aligned profiles |${P}_{a1}\ \mathrm{and}\ {P}_{a2}$| |
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