生物信息学实验三核酸序列分析常用分子信息学软件使用.docx
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生物信息学实验三核酸序列分析常用分子信息学软件使用.docx
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生物信息学实验三核酸序列分析常用分子信息学软件使用
实验三、核酸序列分析、常用分子信息学软件使用
1、用BioEdit等软件进行序列分析
用BioEdit打开FASTA格式的序列
Sequence-->Nucleicacid-->
1)Sequence-->Nucleicacid-->Nucleotidcomposition
DNAmolecule:
gi|725605238|ref|XM_010330964.1|PREDICTED:
Saimiriboliviensisboliviensisinterferon,lambda3(IFNL3),mRNA
Length=744basepairs
MolecularWeight=227718.00Daltons,singlestranded
MolecularWeight=453776.00Daltons,doublestranded
G+Ccontent=61.56%
A+Tcontent=38.44%
NucleotideNumberMol%
A14118.95
C25133.74
G20727.82
T14519.49
2)Sequence-->Nucleicacid-->Basecompositionandmassexport(monoisotopic)
TitleLENGTHAGCTGapOtherMono_exact_massBaseCompOppositeStrand_exact_massOppositeStrand_BaseComp
gi|725605238|ref|XM_010330964.1|PREDICTED:
Saimiriboliviensisboliviensisinterferon,lambda3(IFNL3),mRNA74414120725114500228830.3528025A141G207C251T145230626.6695859A145G251C207T141
3)Sequence-->Nucleicacid-->Basecompoeitionandmassexportwithaveragemasses
TitleLENGTHA_COUNTG_COUNTC_COUNTT_COUNTGAP(notusedindb)OTHER_COUNTMONO_EXACT_MASSBASE_COMPOPPOSITE_STRAND_MASSOPPOSITE_STRAND_BASE_COMPSEQUENCE(notusedindb)OppositeStrand_Ave_massOppositeStrand_BaseComp
gi|725605238|ref|XM_010330964.1|PREDICTED:
Saimiriboliviensisboliviensisinterferon,lambda3(IFNL3),mRNA74414120725114500228939.3442020A141G207C251T145230736.4659940A145G251C207T141
4)Sequence-->Nucleicacid-->complement
CACTGTCGGAGTCTCACCCCAGGAAGACGACTGCTTCTGGTCTCTAGTCTTTACTTTGCTCCGTACTCGTCCCCGACGTACCGTCACGACCACGACTACCGGTGTCACGACTGACAGTGACCTCGTCAAGGACAGTGGTCCGGGGGGTCCCGGGAGGGCCTACGTTCCCCGACGGTGTATCGGGTCAAGTTCAGAGACAGGGGTGTCCTCGACGTTCGGAAATTCTCTCGGTTTCTACGGAATCTTCTCAGCGAAGACGACTTCCTGACGTCCACGGCGAGGGCGGAGAAGGGGTCCTGGACCCTGGACTCCGTCGACGTCCACTCCCTCGCGGGGCACCGGAACCTCCGACTCGACCGGGACTGCGACCTCCAAGACCTCCGGTGGCGACTGTTACTGTACCGGGACCCACTGCAGGACCTGGCCGGGGAAGTGTGGGACGTGGTGCAGGAGAGGGTCGAGGCCCGGACACAGGTCGGAGTCGGGTGCCGTCCCGGGTCCGGGACCCCAGCGGAGGTGGTGACCGACGTGGCCGAGGTCCTCCGGGGTTTTTTCCTCAGGAGACCGACGGACCTCCGGAGACAGTGGAAGTTGGAGAAGGCGGAGGAGTGCGCCCTGGACTTTACGCAGCGGTCGCCCCTGGACACACGGACTGGAAGGGTGGAGGGACGGTGGGTAGTACGTTAGACTCTAAAATAAATATGTAGTTGGTGAACAGAATTAAATAACGGTGGGTTAGCGATA
5)Sequence-->Nucleicacid-->reversecomplement
TATCGCTAACCCACCGTTATTTAATTCTGTTCACCAACTACATATTTATTTTAGAGTCTAACGTACTACCCACCGTCCCTCCACCCTTCCAGTCCGTGTGTCCAGGGGCGACCGCTGCGTAAAGTCCAGGGCGCACTCCTCCGCCTTCTCCAACTTCCACTGTCTCCGGAGGTCCGTCGGTCTCCTGAGGAAAAAACCCCGGAGGACCTCGGCCACGTCGGTCACCACCTCCGCTGGGGTCCCGGACCCGGGACGGCACCCGACTCCGACCTGTGTCCGGGCCTCGACCCTCTCCTGCACCACGTCCCACACTTCCCCGGCCAGGTCCTGCAGTGGGTCCCGGTACAGTAACAGTCGCCACCGGAGGTCTTGGAGGTCGCAGTCCCGGTCGAGTCGGAGGTTCCGGTGCCCCGCGAGGGAGTGGACGTCGACGGAGTCCAGGGTCCAGGACCCCTTCTCCGCCCTCGCCGTGGACGTCAGGAAGTCGTCTTCGCTGAGAAGATTCCGTAGAAACCGAGAGAATTTCCGAACGTCGAGGACACCCCTGTCTCTGAACTTGACCCGATACACCGTCGGGGAACGTAGGCCCTCCCGGGACCCCCCGGACCACTGTCCTTGACGAGGTCACTGTCAGTCGTGACACCGGTAGTCGTGGTCGTGACGGTACGTCGGGGACGAGTACGGAGCAAAGTAAAGACTAGAGACCAGAAGCAGTCGTCTTCCTGGGGTGAGACTCCGACAGTG
6)Sequence-->Nucleicacid-->DNA-->RNA
GUGACAGCCUCAGAGUGGGGUCCUUCUGCUGACGAAGACCAGAGAUCAGAAAUGAAACGAGGCAUGAGCAGGGGCUGCAUGGCAGUGCUGGUGCUGAUGGCCACAGUGCUGACUGUCACUGGAGCAGUUCCUGUCACCAGGCCCCCCAGGGCCCUCCCGGAUGCAAGGGGCUGCCACAUAGCCCAGUUCAAGUCUCUGUCCCCACAGGAGCUGCAAGCCUUUAAGAGAGCCAAAGAUGCCUUAGAAGAGUCGCUUCUGCUGAAGGACUGCAGGUGCCGCUCCCGCCUCUUCCCCAGGACCUGGGACCUGAGGCAGCUGCAGGUGAGGGAGCGCCCCGUGGCCUUGGAGGCUGAGCUGGCCCUGACGCUGGAGGUUCUGGAGGCCACCGCUGACAAUGACAUGGCCCUGGGUGACGUCCUGGACCGGCCCCUUCACACCCUGCACCACGUCCUCUCCCAGCUCCGGGCCUGUGUCCAGCCUCAGCCCACGGCAGGGCCCAGGCCCUGGGGUCGCCUCCACCACUGGCUGCACCGGCUCCAGGAGGCCCCAAAAAAGGAGUCCUCUGGCUGCCUGGAGGCCUCUGUCACCUUCAACCUCUUCCGCCUCCUCACGCGGGACCUGAAAUGCGUCGCCAGCGGGGACCUGUGUGCCUGACCUUCCCACCUCCCUGCCACCCAUCAUGCAAUCUGAGAUUUUAUUUAUACAUCAACCACUUGUCUUAAUUUAUUGCCACCCAAUCGCUAU
7)Sequence-->Nucleicacid-->RNA-->DNA
GTGACAGCCTCAGAGTGGGGTCCTTCTGCTGACGAAGACCAGAGATCAGAAATGAAACGAGGCATGAGCAGGGGCTGCATGGCAGTGCTGGTGCTGATGGCCACAGTGCTGACTGTCACTGGAGCAGTTCCTGTCACCAGGCCCCCCAGGGCCCTCCCGGATGCAAGGGGCTGCCACATAGCCCAGTTCAAGTCTCTGTCCCCACAGGAGCTGCAAGCCTTTAAGAGAGCCAAAGATGCCTTAGAAGAGTCGCTTCTGCTGAAGGACTGCAGGTGCCGCTCCCGCCTCTTCCCCAGGACCTGGGACCTGAGGCAGCTGCAGGTGAGGGAGCGCCCCGTGGCCTTGGAGGCTGAGCTGGCCCTGACGCTGGAGGTTCTGGAGGCCACCGCTGACAATGACATGGCCCTGGGTGACGTCCTGGACCGGCCCCTTCACACCCTGCACCACGTCCTCTCCCAGCTCCGGGCCTGTGTCCAGCCTCAGCCCACGGCAGGGCCCAGGCCCTGGGGTCGCCTCCACCACTGGCTGCACCGGCTCCAGGAGGCCCCAAAAAAGGAGTCCTCTGGCTGCCTGGAGGCCTCTGTCACCTTCAACCTCTTCCGCCTCCTCACGCGGGACCTGAAATGCGTCGCCAGCGGGGACCTGTGTGCCTGACCTTCCCACCTCCCTGCCACCCATCATGCAATCTGAGATTTTATTTATACATCAACCACTTGTCTTAATTTATTGCCACCCAATCGCTAT
8)Sequence-->Nucleicacid-->Translate
Frame1:
>gi|725605238|ref|XM_010330964.1|PREDICTED:
Saimiriboliviensisboliviensisinterferon,lambda3(IFNL3),mRNA
1GTGACAGCCTCAGAGTGGGGTCCTTCTGCTGACGAAGACCAGAGA45
1ValThrAlaSerGluTrpGlyProSerAlaAspGluAspGlnArg15
46TCAGAAATGAAACGAGGCATGAGCAGGGGCTGCATGGCAGTGCTG90
16SerGluMetLysArgGlyMetSerArgGlyCysMetAlaValLeu30
91GTGCTGATGGCCACAGTGCTGACTGTCACTGGAGCAGTTCCTGTC135
31ValLeuMetAlaThrValLeuThrValThrGlyAlaValProVal45
136ACCAGGCCCCCCAGGGCCCTCCCGGATGCAAGGGGCTGCCACATA180
46ThrArgProProArgAlaLeuProAspAlaArgGlyCysHisIle60
181GCCCAGTTCAAGTCTCTGTCCCCACAGGAGCTGCAAGCCTTTAAG225
61AlaGlnPheLysSerLeuSerProGlnGluLeuGlnAlaPheLys75
226AGAGCCAAAGATGCCTTAGAAGAGTCGCTTCTGCTGAAGGACTGC270
76ArgAlaLysAspAlaLeuGluGluSerLeuLeuLeuLysAspCys90
271AGGTGCCGCTCCCGCCTCTTCCCCAGGACCTGGGACCTGAGGCAG315
91ArgCysArgSerArgLeuPheProArgThrTrpAspLeuArgGln105
316CTGCAGGTGAGGGAGCGCCCCGTGGCCTTGGAGGCTGAGCTGGCC360
106LeuGlnValArgGluArgProValAlaLeuGluAlaGluLeuAla120
361CTGACGCTGGAGGTTCTGGAGGCCACCGCTGACAATGACATGGCC405
121LeuThrLeuGluValLeuGluAlaThrAlaAspAsnAspMetAla135
406CTGGGTGACGTCCTGGACCGGCCCCTTCACACCCTGCACCACGTC450
136LeuGlyAspValLeuAspArgProLeuHisThrLeuHisHisVal150
451CTCTCCCAGCTCCGGGCCTGTGTCCAGCCTCAGCCCACGGCAGGG495
151LeuSerGlnLeuArgAlaCysValGlnProGlnProThrAlaGly165
496CCCAGGCCCTGGGGTCGCCTCCACCACTGGCTGCACCGGCTCCAG540
166ProArgProTrpGlyArgLeuHisHisTrpLeuHisArgLeuGln180
541GAGGCCCCAAAAAAGGAGTCCTCTGGCTGCCTGGAGGCCTCTGTC585
181GluAlaProLysLysGluSerSerGlyCysLeuGluAlaSerVal195
586ACCTTCAACCTCTTCCGCCTCCTCACGCGGGACCTGAAATGCGTC630
196ThrPheAsnLeuPheArgLeuLeuThrArgAspLeuLysCysVal210
631GCCAGCGGGGACCTGTGTGCCTGACCTTCCCACCTCCCTGCCACC675
211AlaSerGlyAspLeuCysAlaEndProSerHisLeuProAlaThr225
676CATCATGCAATCTGAGATTTTATTTATACATCAACCACTTGTCTT720
226HisHisAlaIleEndAspPheIleTyrThrSerThrThrCysLeu240
721AATTTATTGCCACCCAATCGCTAT744
241AsnLeuLeuProProAsnArgTyr
Eachcodonisreadasleftnucleotide,topnucleotide,rightnucleotide
Eachentryisorganizedasfollows:
Thenumberofoccurrencesofthecodoninthesequence
Preferenceofthatcodoninorganismrepresentedbythecodontable
(asafractionofallcodonscodingforthesameaminoacid)
Three-lettercodefortheaminoacidcodedforaccordingtothecodontable
|ACGT|
-----------------------------
A|4321|A
|0.760.120.040.07|
|LysThrArgIle|
-----------------------------
A|1721|C
|0.610.430.270.46|
|AsnThrSerIle|
-----------------------------
A|4395|G
|0.240.230.031|
|LysThrArgMet|
-----------------------------
A|3301|T
|0.390.210.130.47|
|AsnThrSerIle|
-----------------------------
C|1310|A
|0.310.20.050.03|
|GlnProArgLeu|
-----------------------------
C|89610|C
|0.480.10.370.1|
|HisProArgLeu|
-----------------------------
C|91420|G
|0.690.550.080.55|
|GlnProArgLeu|
-----------------------------
C|2503|T
|0.520.160.420.1|
|HisProArgLeu|
-----------------------------
G|3510|A
|0.70.220.090.17|
|GluAlaGlyVal|
-----------------------------
G|101747|C
|0.410.250.40.2|
|AspAlaGlyVal|
-----------------------------
G|11026|G
|0.30.340.130.34|
|GluAlaGlyVal|
-----------------------------
G|3332|T
|0.590.190.380.29|
|AspAlaGlyVal|
-----------------------------
T|0322|A
|0.620.120.30.11|
|EndSerEndLeu|
-----------------------------
T|0564|C
|0.470.170.570.49|
|TyrSerCysPhe|
-----------------------------
T|0142|G
|0.090.1310.11|
|EndSerTrpLeu|
-----------------------------
T|2432|T
|0.530.190.430.51|
|TyrSerCysPhe|
-----------------------------
Frame2:
>gi|725605238|ref|XM_010330964.1|PREDICTED:
Saimiriboliviensisboliviensisinterferon,lambda3(IFNL3),mRNA
2TGACAGCCTCAGAGTGGGGTCCTTCTGCTGACGAAGACCAGAGAT46
1EndGlnProGlnSerGlyValLeuLeuLeuThrLysThrArgAsp15
47CAGAAATGAAACGAGGCATGAGCAGGGGCTGCATGGCAGTGCTGG91
16GlnLysEndAsnGluAlaEndAlaGlyAlaAlaTrpGlnCysTrp30
92TGCTGATGGCCACAGTGCTGACTGTCACTGGAGCAGTTCCTGTCA136
31CysEndTrpProGlnCysEndLeuSerLeuGluGlnPheLeuSer45
137CCAGGCCCCCCAGGGCCCTCCCGGATGCAAGGGGCTGCCACATAG181
46ProGlyProProGlyProSerArgMetGlnGlyAlaAlaThrEnd60
182CCCAGTTCAAGTCTCTGTCCCCACAGGAGCTGCAAGCCTTTAAGA226
61ProSerSerSerLeuCysProHisArgSerCysLysProLeuArg75
227GAGCCAAAGATGCCTTAGAAGAGTCGCTTCTGCTGAAGGACTGCA271
76GluProLysMetProEndLysSerArgPheCysEndArgThrAla90
272GGTGCCGCTCCCGCCTCTTCCCCAGGACCTGGGACCTGAGGCAGC316
91GlyAlaAlaProAlaSer
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