Instale o programa Mega (versão Windows) em seu computador
(Website do Mega),
fazendo o registro em seu nome com seu email.
1. Abra o programa.
2. Abra o arquivo de sequências, em formato "fasta", trecho1.fas. Trata-se de um trecho do
genoma mitocondrial de espécies de mamíferos, onde:
Ovis = Ovis aries,
ovelha, Peryssodactyla, Bovidae
Oryctolagus = Oryctolagus
cuniculus, coelho selvagem europeu, Logomorpha, Leporidae
Dasypus = Dasypus novemcinctus,
tatu, Xenarthra, Dasypodidae
Ceratotherium = Ceratotherium
simum, rinoceronte branco, Perissodactyla,
Rhinocerotidae
Macropus = Macropus robustus,
canguru, Marsupialia, Macropodidae
E_asinus, Equus asinus,
jumento, Peryssodactyla, Equidae
Rhinoceros = Rhinocerus
unicornis, Rinoceronte indiano,
Perissodactyla, Rhinocerotidae
E_caballus, Equus caballus,
cavalo, Peryssodactila Equidae.
Didelphis = Didelphis
virginiana, gambá ("opossum"), Marsupialia,
Didelphidae.
Halichoerus = Halichoerus grypus, foca cinzenta, Pinipedia, Phocidae
Homo = Homo sapiens,
gente, Primates, Hominidae
P_troglodytes = Pan troglodytes,
chimpanzé, Primates, Hominidae
Phoca = Phoca vitulina, foca comum, Pinipedia, Phocidae
B_physalus = Balaenoptera
physalus, baleia fin, Cetacea
B_musculus =Balaenoptera
musculus, baleia azul, Cetacea
Bos = Bos taurus, vaca,
Peryssodactyla, Bovidae
Ornithorhynchus = Ornithorhynchus anatinus, ornitorrinco, Monotremata
Gorilla, Gorilla gorilla,
gorila,
Primates, Pongidae
Erinaceus = Erinaceus europaeus,
ouriço cacheiro, Insectivora, Erinaceidae.
Felis = Felis catus,
gato doméstico Carnivora, Felidae
Hylobates = Hylobates lar,
gibão,
Primates, Hylobatidae.
Pongo = Pongo pygmaeus, Orangotango, Primates, Hominidae
P_paniscus = Pan paniscus,
chimpanzé pigmeu ou bonobo, Primates, Hominidae
Rattus = Rattus norvegicus,
rato, Rodentia, Muridae
Sus = Sus scrofa, porco, Artyodactyla, Suidae
Mus = Mus musculus, camundongo, Rodentia, Muridae
Papio = Papio hamadryas,
babuíno, Primates, Cercopithecidae.
Loxodonta = Loxodonta africana, elefante, Proboscidae
Hippopotamus = Hippopotamus
amphibius, Artiodactyla, Hippopotamidae
Canis = Cannis familiaris,
cachorro doméstico, Carnivora, Canidae.
Artibeus, Artibeus jamaicensis,
morcego jamaicano, Chiroptera, Phyllostomidae
As sequências correspondem a uma série de genes do
genoma mitocondrial que correspondem a tRNAs, rRNA e a
proteína ND1, o registro de Ovis começa assim:
LOCUS
NC_001941
16616
bp DNA circular MAM
21-APR-2009
DEFINITION Ovis aries mitochondrion, complete genome.
ACCESSION NC_001941
VERSION NC_001941.1 GI:5835554
DBLINK Project:10764
KEYWORDS .
SOURCE mitochondrion Ovis aries
(sheep)
ORGANISM Ovis aries
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Laurasiatheria; Cetartiodactyla; Ruminantia;
Pecora; Bovidae; Caprinae; Ovis.
REFERENCE 1 (bases 1 to 16616)
AUTHORS Hiendleder,S., Lewalski,H., Wassmuth,R.
and Janke,A.
TITLE The complete mitochondrial
DNA sequence of the domestic sheep (Ovis
aries) and comparison with the other major ovine haplotype
JOURNAL J. Mol. Evol. 47 (4), 441-448 (1998)
PUBMED 9767689
REFERENCE 2 (bases 1 to 16616)
AUTHORS Hiendleder,S.
TITLE A low rate of replacement
substitutions in two major Ovis aries
mitochondrial genomes
JOURNAL Anim. Genet. 29 (2), 116-122 (1998)
PUBMED 9699271
REFERENCE 3 (bases 1 to 16616)
AUTHORS Hiendleder,S., Mainz,K., Plante,Y. and
Lewalski,H.
TITLE Analysis of mitochondrial DNA
indicates that domestic sheep are
derived from two different ancestral maternal sources: no evidence
for contributions from urial and argali sheep
JOURNAL J. Hered. 89 (2), 113-120 (1998)
PUBMED 9542158
REFERENCE 4 (bases 1 to 16616)
CONSRTM NCBI Genome Project
TITLE Direct Submission
JOURNAL Submitted (12-JUL-2004) National Center
for Biotechnology
Information, NIH, Bethesda, MD 20894, USA
REFERENCE 5 (bases 1 to 16616)
AUTHORS Hiendleder,S., Wassmuth,R. and
Lewalski,H.
TITLE Direct Submission
JOURNAL Submitted (19-AUG-1998) Animal Breeding
and Genetics,
Justus-Liebig-University, Ludwigstr. 21B, Giessen 35390, Germany
REMARK Sequence update by submitter
REFERENCE 6 (bases 1 to 16616)
AUTHORS Hiendleder,S., Wassmuth,R. and
Lewalski,H.
TITLE Direct Submission
JOURNAL Submitted (26-JUN-1997) Animal Breeding
and Genetics,
Justus-Liebig-University, Ludwigstr. 21B, Giessen 35390, Germany
COMMENT PROVISIONAL REFSEQ: This record
has not yet been subject to final
NCBI review. The reference sequence was derived from AF010406.
FEATURES
Location/Qualifiers
source
1..16616
/organism="Ovis
aries"
/organelle="mitochondrion"
/mol_type="genomic
DNA"
/strain="Merinolandschaf"
/db_xref="taxon:9940"
/tissue_type="liver"
/note="haplotype
B (European type)"
tRNA
1..68
/product="tRNA-Phe"
rRNA
69..1026
/product="12S
ribosomal RNA"
tRNA
1027..1093
/product="tRNA-Val"
rRNA
1094..2667
/product="16S
ribosomal RNA"
tRNA
2668..2742
/product="tRNA-Leu"
/codon_recognized="UUR"
gene
2745..3699
/gene="ND1"
/db_xref="GeneID:808249"
CDS
2745..3699
/gene="ND1"
/note="TAA
stop codon is completed by the addition of 3' A
residues
to the mRNA"
/codon_start=1
/transl_except=(pos:3699,aa:TERM)
/transl_table=2
/product="NADH
dehydrogenase subunit 1"
/protein_id="NP_008406.1"
/db_xref="GI:5835555"
/db_xref="GeneID:808249"
/translation="MFMINVLTLIIPILLAVAFLTLVERKVLGYMQFRKGPNVVGPYG
LLQPIADAIKLFIKEPLRPATSSISMFILAPILALTLALTMWIPLPMPYPLINMNLGV
LFMLAMSSLAVYSILWSGWASNSKYALIGALRAVAQTISYEVTLAIILLSVLLMNGSF
TLSTLIITQEQVWLIFPAWPLAMMWFISTLAETNRAPFDLTEGESELVSGFNVEYAAG
PFALFFMAEYANIIMMNIFTTTLFLGAFHNPYMPELYTINFTIKSLLLSITFLWIRAS
YPRFRYDQLMHLLWKNFLPLTLALCMWHVSLPILLSSIPPQT"
tRNA
3701..3769
/product="tRNA-Ile"
tRNA
complement(3767..3838)
/product="tRNA-Gln"
tRNA
3841..3909
/product="tRNA-Met"
3. Selecione algumas sequências (cerca de 15) e realize um
alinhamento múltiplo com o ClustalW, fornecendo as
penalidades de abertura e extensão de lacunas para
alinhamentos par a par e múltiplo. Verifique o tempo gasto.
Visualize o alinhamento e grave-o em arquivo.
4. Repita a etapa 3 quantas vezes achar conveniente com outros
parâmetros (penalidades de abertura e extensão de
lacunas), tentando achar as combinações que produzam
resultados mais satisfatórios.
5. Localize as regiões mais problemáticas e
identifique-as.
6. Repita os ítens 3 a 5 com o programa Muscle,
também interno ao Mega.
7. Compare os resultados.
8. (Opcional) Realize os alinhamentos com o programa JalView (Website do Jalview)
e os compare com aqueles obtidos com o ClustalW e com o Muscle.