BIOINFORMATICS

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[CELLULAR AND MOLECULAR BIOLOGY]

MTEB 2202

PRACTICAL 1
Bioinfomatics part B : Repetitive Elements

OBJECTIVES
To look up the repetitive elements of DYNC1I1 gene in human chromosome 7

METHOD
1. First, get the FASTA sequence of NC_000007.12

2. Copy the sequence at around 50 lines senquence to Word Document

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[CELLULAR AND MOLECULAR BIOLOGY]

MTEB 2202

CAGTGGAAAAATATTTGGATACGAGCATATATCCTTGCCCCGCTTTTTCATGTTTGAAGCAGCCTTACTC TCATGAGTGTAAGTGAGCACCTGAAAATGAGTTAAGGTCACACAGTGTGTGCTTTCATAAGCCACCATAT AATTGCCAGAATGACCGTTTATATTTTGGGGGAAACTTTAGGACTTCTGTCTTCCCGGAGAATAATCTGG CACTTAAAGCTGTGTACAGTCAGCCTAACCTCCTCTCACTTGCACATGGGAGCCCTTGGACTCAGCCCGT TGGTCTCTTCACTCTTCACTATGGTCAAATCACATTCCTGTCCCTGTGCCTGTGGTCTTGCTCTTCCCTA CTCTTCCAGTGACATTCCCTCTGCTGTTTAACTAGCCCCAACCCCACCCATTCCACTGCTGAAAGCCCAA GACTCATCTCCTCACAAATAGTTCCTACAGCCTCTTCAGTTCAGTTTCCCGTCCTCATTCTCTGCCTTTT ACCAGGACTGTATCGGTTCATTTGGTCCTTGTTCTCAAGTAGACCACAGGGCAGTCTACTTGAGAATGAA TGTCTCAATCAACTGTTTTTTTTTTTTTTGGTCTCAGAATATATATATATATTCAACATTCAATAAATAT TGTTTAACAGAATTATCAGTTACATGGAAAAGTAGAAAAGCATTGTCAAATTGAGTTCTATTTTTTGAAA ACAAAATATGAGTAGCAAGAAATAAATAGAATGAAAACAATACTTGCAAATTATGTAAGTAAATTCAACC AAATGTGACAGATGGAAATTTTTATAATTGTTAACTATGTTTTATTTACTTTTTATAACATATTTTAACT AATACAAAATAGTGTTTAGGTGTTGGCAAATTTAGTTAAGCAGTCATGGGTATCTTATTTAAGGAAGAAG ATCATGAAATGCTCTTTTTAACCTTGTTAAACAACCACGGGAGGAGATGGAGACTACCCGTGCAAGGAGA CTGCACTTATAGAGTTTAATAAAAATGTATCTATCATAAACTTAGTTTCTAAAACAATAAAATATTTGTT TATAGAACCCTATCATGGAGCTCTCTAGTTTTGCAAATGAGCTATTTTTCCACATTTCATTCTATAAGCA AGCATTTGACACCTAAATAGCGAGCTGTAGATTTAACATCTATTGTGTTATACCCTAAATATCAAAGATT TAAAAAAACACTGGTAGGCACTATTGATGAGACCATGAAAAGAGTTTTGAGGAAAATAATGCAGCCTTTT GTACCAGAAAACAGTAATAATAAAAAAAGTGAATGACTCATGATGCTCATAATACACCAAATGGCTAAAT ATTACTGGTTGAACAACTCTTCAACTCTGATTTCCTGAGCATTTTTCTAGCTAATCTGTAGGATTTAGCA TTCAGTCGTCTGGCCTCTCTGGGTGGGGCGAGGGGTGGGGGTTCATCCATAGCCAAATGCAGGAGAGCCT CCTTGATTGCTCACTAGCAGCCCAGGAATCTAGGACTCCTGGTGATTTTCCCCAGCGGTTGGTTTAGAAA GTGTGCAGGCTTAGATACATGGAGAGCAGAGTGCTCGGCAGGGCATCCCCAGTGGAGCAGCACTGGAAAG CTGGCATCACCACATTATCATATCCAGAGTCATAGTAAAATGTACCTTGTTAAATGTGATCTTGGCCTGT AAAGAAACAAAAGACTACTTTTAAGACAAAACATAAACTGCATTACAAGCCAGGGAGTAGGGTTGATGGG AGGACTATGGGACGGCAGTGGGGGGAAATTAGAGAGTTGGGCACAGCTCTCCCAGACAGTGTCTGAAGAA AAAAGACTGTGTTTGTTCCTGGAACAGACCAAAAAGGGAGGATGTGAAGACTGATGAAATACCAAAGAGA GACTTGGGATAAAGACAGTTCTAATTGAAAGGGAAAGAATGGCAGGACAAAAGTTCATGGGGAGGAGAAA GAGGAGCTCAGTAATGAGACAGCAGAAAAAAAAAAAAAAACCCAGCTGAAAACTCTGGAGAAACTTGGAG GGTGGGAGGGGGGTGGGGGGGGGGGGCGGGGCGGGAAGGGAAAATACAACTTGGATATTTTTCGAACTCT AGCAGCAACAAGGATGTTTCCTAACCACATCTTTGGCTGTGAGAACCTTGTTGTTGGAAATTACATGTAA

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[CELLULAR AND MOLECULAR BIOLOGY]
AACAAAAATGTGTCCAGATTCCATTTTGTATCTATTCATTTTTAAACCTGTGTTTATTGGGCATCTTCTG

MTEB 2202

TGTGACTACATTGCACTACAGCCGGGGTTTCAGGGGGCATGGCTTGGGCATGCTCACACTCTGCTGTCCT GGAATGTGAAGGAATTGGATCCTGGGCCATGAAAGGAAAAGAGGAAGGAGGAAGAGAAGGACCTGGCAGA AGGAATGAGGGTGAAGCTGGAGTGACTTTTATAAAATATAAATAAATCGCATCACCCCCTTGCTTAAAAC CCTTCCGTGGTATCTGGTGCTCTTTTTTTAAGGAAAAATTGTATTATTTTAATTATTTTTATGTACAGAA AACTCAACAGTGTACATTTAAGCCACTTTGGTGTGACAAGTTCTTTAACCTTTGCCTCTTCGAGCTTGGC AGTGCGAGCCACAGACTTGGGACCCAGCATCTGGTTGCTCTTGAGATCAGTCCAAACTCCTTGCTAGGTG CTTTGAGACCTGCGTTACCTGGACTGAGCCTCGTTCTCCATCCTGTTTCATCTGTCTTTCTCTCTCTTTC TCAGATGGTCATTTTGGGGTTGCGCTTGATTCAAGTGCACTTCAGAGGTGGTCCTGGGTCAGAAGACTGG CTGCAGAGCTGGCCCCACTGTTAGGCCACTGCAAGAATCTCCTTGCCTCTTTTCCTTGCATTGTCCCCAC CTTGTCACCCCTATAGGGATGCTGTAAGGATGAAGGCTTTGCTCTTGCTTTGTTTGACCTATCTGAATTG GAGGACTCAGAATTCTTCTTTCTCCTTTCATTTCCACTCAATATTGAGTCCCTCCTAAGGCCTGTGAATT ATTTCTTCATATTTCTTGGATCCTGTACCTTTCATGTCATTCCCAGAGCTAAAACCCTAACTCTAGCCAT TATTACATCACACCTGAAATAATACAGCTTCCTAAATGCTACCCCCATCTGTTCCTCCTCCCACCCAGAT TAACTGGCATTCAGGACTTCTGTGTCCAGGAGCCAGATGTTTTGTATTTTCTGTTATATTATCTGACAGC CCTAGCCCTTCATCCATGCATGTATAATCCATGTAAAGTGGACACTTATCCCTGGAAGTGGTAAGTCTTG AGCTGGGCTCTGAGGCATGGATTAAGGTTTAGAGAGGCTGAAGGGCAGGACAGGGCCTCCTGGGCATTAG CAAGGGTTTGGAGGCAGGTGTGCTGGGGCCAGTAAGTAGAGCAGAGAGTAATGGGAAATCAGGTTGCATT GGGCTTTGGCTGCCTTGTCAAGGCATTAGAAGAATAGGAATCAGTACAAGAATTATGGACATTTATAGGT TACAGACTGGGTTCAAGTCCTATTGCTGTCACTTATTAGTTACATGAACTTTGAAAGTACTCAGATTTCT CACCTGTTAAAGAGGCAATAGCACCCCTCACAGGGTTGTTTTGAAAATGAAATCAGATCATACATACATG TAGCTCACAGTTGCTCATGACTAGCATGTAGTAGAGGTTGGCCGTCGTAATATTGGCCATCATCATCTTT ATCATCATGACCTTTGTCATGATCATTATTTTTTTGGATAATGGTGAATATTAAAGATTTGGAATTTTTT AAAAACGAGAGGTGAGAAAGGATAGCATGGTAAAAGCTATGCTTTGAGGGTGTCACATTTTTAGGAGGTT AGCTTGGAAGAGTTCTGAAGAGGCATTCTCACTCAAGTGTGGGGATAGCTGGGCTACTCTGCCAACAGCT ATGATGATGTTTCCAGACACAGTATAAAAAAATAGACCAACAAGGCTTGATAATCCACAATTGTCAAAAA TTAGAACAGAGCAGGAGTCTTGAAGCCAGGGAAACTTCACAGTTTTGGAGGTTCGAACTTGTCAGTGACC AAAGTGAAGTGATCTGAAGCCAGGAGGTAAGTCATGATGGCGAGGAGAAGTCCAGTCCAGAGGAGGAAGG CATTCAGATTCTGAGAATGAGGCAGATTATTGGAGTGGGGCCGGTGGAGAGACCCCACAGAGGTGACACA GGTGACACTGAGGCAGTGGTGGTATGTACTTCTCTGCTTCAGTTAAGGGTCAAAAAAGGCTGACCAGAGG TGAGAAGAAGGAAAGCAAGGAGGGAAGGAACAATATCAAGCACTCCTCCTGAGAAGTGGCTGATTGGAAA TGTGCCCATGAAGGACACAGAGGCCCAAGCTTACATTTAGGAAATAGTTGAAACACTAGGGAAGCAGGAA

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[CELLULAR AND MOLECULAR BIOLOGY]

MTEB 2202

3. Go to Repeatmasker and choose Repeatmasking on the left side column.

4. Enter FASTA sequences by leaving all the other sequences and click

on Submit Sequences

5. The result of Submit Sequences will be shown of summary and others file (Annotation, Masked and Alignment).

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[CELLULAR AND MOLECULAR BIOLOGY]

MTEB 2202

RESULT
1. Summary of the sequences

Summary:
================================================== file name: RM2sequpload_1219311372 sequences: 1 total length: 4410 bp (4410 bp excl N/X-runs) GC level: 42.22 % bases masked: 345 bp ( 7.82 %) ================================================== number of length percentage elements* occupied of sequence -------------------------------------------------SINEs: 1 164 bp 3.72 % ALUs 0 0 bp 0.00 % MIRs 1 164 bp 3.72 % LINEs: LINE1 LINE2 L3/CR1 LTR elements: ERVL ERVL-MaLRs ERV_classI ERV_classII DNA elements: hAT-Charlie TcMar-Tigger Unclassified: 1 0 1 0 0 0 0 0 0 0 0 0 0 66 0 66 0 0 0 0 0 0 bp bp bp bp bp bp bp bp bp 1.50 0.00 1.50 0.00 0.00 0.00 0.00 0.00 0.00 % % % % % % % % %

0 bp 0 bp 0 bp 0 bp 230 bp 0 bp

0.00 % 0.00 % 0.00 % 0.00 % 5.22 % 0.00 %

Total interspersed repeats: Small RNA: 0

Satellites: 0 0 bp 0.00 % Simple repeats: 1 42 bp 0.95 % Low complexity: 2 73 bp 1.66 % ==================================================
* most repeats fragmented by insertions or deletions have been counted as one element The query species was assumed to be homo RepeatMasker version open-3.2.6 , default mode run with blastp version 2.0MP-WashU RepBase Update 20080801, RM database version 20080801

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[CELLULAR AND MOLECULAR BIOLOGY]

MTEB 2202

2. Annotation File: RM2sequpload_1219311372.out.html ( NEW XHTML

Format )

3. Defining the repeat : a. L2

b. AT-Rich

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[CELLULAR AND MOLECULAR BIOLOGY]

MTEB 2202

c. MiRb

d. (CAT)n

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[CELLULAR AND MOLECULAR BIOLOGY]

MTEB 2202

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