利用动态规划算法进行两条序列比对

利用动态规划算法进行两条序列比对
实 验 目 的
学会使用EMBOSS 软件包的NEEDLE 和WATER 进行两条序列比对。

实 验 内 容
1. Get the mRNA and protein sequence of Chlorocebus sabaeus and Colobus angolensis
palliates from NCBI.
2. Use Needle to do the sequence alignment in default parameters.
*****Protein Sequence alignment result*****
Program: needle
# Rundate: Sat 28 Sep 2019 16:43:43 # Commandline: needle # -auto # -stdout
# -datafile EBLOSUM62
# -gapopen 10.0 # -gapextend 0.5 # -endopen 10.0 # -endextend 0.5
# -aformat3 pair # -sprotein1 # -sprotein2 # Align_format: pair # Report_file: stdout # Aligned_sequences: 2
# 1: XP_008000870.1 # 2: XP_011811726.1 # Matrix: EBLOSUM62 # Gap_penalty: 10.0 # Extend_penalty: 0.5 # Length: 586
# Identity: 561/586 (95.7%) # Similarity: 572/586 (97.6%) # Gaps: 4/586 ( 0.7%) # Score: 2906.0
***** mRNA Sequence alignment result *****
# Program: needle
# Rundate: Sat 28 Sep 2019 16:47:19 # Commandline: needle # -auto # -stdout
# -datafile EDNAFULL
# -gapopen 10.0 # -gapextend 0.5 # -endopen 10.0 # -endextend 0.5 # -aformat3 pair # -snucleotide1
# -snucleotide2
# Align_format: pair # Report_file: stdout # Aligned_sequences: 2
# 1: XM_008002679.1 # 2: XM_011956336.1 # Matrix: EDNAFULL
# Gap_penalty: 10.0 # Extend_penalty: 0.5 # Length: 2594
# Identity: 2505/2594 (96.6%) # Similarity: 2505/2594 (96.6%) # Gaps: 27/2594 ( 1.0%) # Score: 12207.5
a. After alignment, we have found that the identity and the gaps between two mRNAs were higher than protein, but the similarity of mRNA was lower than protein.
b. The two sequences are closely related.
3. Use Water to do the sequence alignment in default parameters.
*****Protein Sequence alignment result*****
# Program: water
# Rundate: Sat 28 Sep 2019 16:52:02 # Commandline: water # -auto # -stdout
# -datafile EBLOSUM62
# -gapopen 10.0 # -gapextend 0.5 # -aformat3 pair
# -sprotein1 # -sprotein2 # Align_format: pair # Report_file: stdout
# Aligned_sequences: 2 # Matrix: EBLOSUM62
# Gap_penalty: 10.0 # Extend_penalty: 0.5 #
# Length: 582
# Identity: 561/582 (96.4%) # Similarity: 572/582 (98.3%) # Gaps: 0/582 ( 0.0%) # Score: 2906.0
*****mRNA Sequence alignment result*****
# Program: water
# Rundate: Sat 28 Sep 2019 16:53:55 # Commandline: water # -auto # -stdout
# -datafile EDNAFULL
# -gapopen 10.0 # -gapextend 0.5 # -aformat3 pair
# -snucleotide1 # -snucleotide2 # Align_format: pair # Report_file: stdout
#
# Aligned_sequences: 2 # Matrix: EDNAFULL
# Gap_penalty: 10.0 # Extend_penalty: 0.5 #
# Length: 2592
# Identity: 2505/2592 (96.6%) # Similarity: 2505/2592 (96.6%) # Gaps: 25/2592 ( 1.0%) # Score: 12207.5
a. After alignment, we have found that the identity and the gaps between two mRNAs were higher than protein, but the similarity of mRNA was lower than protein. ( THE SAME TO Needle )
b. The two sequences are closely related.
c. Higher identity and similarity than Needle.
4. Do the protein sequence alignment and change the original parameters.
Eg: We used the needle to do the protein sequence alignment and changed the GAP_OPEN from 10 to 1.
# Program: needle
# Rundate: Sat 28 Sep 2019 16:58:37 # Commandline: needle # -auto # -stdout
# -datafile EBLOSUM62
# -gapopen 1.0 # -gapextend 0.5 # -endopen 10.0 # -endextend 0.5
# -aformat3 pair
# -sprotein1 # -sprotein2 # Align_format: pair # Report_file: stdout #
# Aligned_sequences: 2 # Matrix: EBLOSUM62
# Gap_penalty: 1.0 # Extend_penalty: 0.5 #
# Length: 588 # Identity: 561/588 (95.4%) # Similarity: 572/588 (97.3%) # Gaps: 8/588 ( 1.4%)
# Score: 2908.0
a. We can get a consequence that the identity, gaps and similarity between the protein sequences become lower, but the score become higher. ( Were more distinct but got higher score )
b. Moreover, we have changed other 4 parameters, but not got any distinct result.
5. Global and local pairwise sequence alignment between human myoglobin and hemoglobin protein sequences.
***Global pairwise sequence alignment***
Protein Sequence Alignment between hemoglobin subunit alpha(beta) and myoglobin(Homo sapiens)
***Local pairwise sequence alignment***
Protein Sequence Alignment between hemoglobin subunit alpha(beta) and myoglobin(Homo sapiens)
实验总结
1.此次实验，我们基本掌握了如何对两条序列进行全局&局部比对，以及根据不同情况对具体参数进行调整的能力。

2.基本掌握了NCBI的Blast以及EMBL-EBI的Needle和Water工具进行序列比对的方法。

附：使用Blast进行蛋白质序列比对的图片一张（Global pairwise sequence alignment）。