生物信息学软件使用

生物信息学软件的使用（以MC4R基因为例）

第一章从NCBI上查找DNA、mRNA、蛋白质序列

一、以猪的黑素皮质素受体4(MC4R, melanocortin-4 re-ceptor)基因为例，介绍如何从NCBI 上查找DNA、mRNA、氨基酸序列。

1.首先查找MC4R的DNA序列。

在百度里输入NCBI，打开后得到的结果如下网页：

在Search 栏输入“MC4R pig”，在下拉菜单里选择Gene，然后点击Search，得到如下结果：

点击第一个ID为397359的链接，得到如下的结果：

可以看到该基因位于猪的1号染色体上，在右下方有个“Go to nucleotide”即进入核酸序列，有三种格式（用红圈标记的），经常用的是“FASTA”和“GenBank”，“FASTA”格式的比较简洁，不包含任何的数字，就全部是碱基，序列的对比和分析是就要用到这种格式；而“GenBank”格式就比较详细，可以查看到很多信息，比如碱基数、mRNA序列、内含子、外显子、CDS，以及氨基酸序列等等之类的。点击GenBank后得到如下结果：

Sus scrofa breed mixed chromosome 1,

Sscrofa10.2 DNA

LOCUS NC_010443 2265 bp DNA linear CON 29-SEP-2013 DEFINITION Sus scrofa breed mixed chromosome 1, Sscrofa10.2.

ACCESSION NC_010443 REGION: complement(178553488..178555752) GPC_000000583 VERSION NC_010443.4 GI:347618793

DBLINK BioProject: PRJNA28993

Assembly: GCF_000003025.5

KEYWORDS RefSeq.

SOURCE Sus scrofa (pig)

ORGANISM Sus scrofa

Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Cetartiodactyla; Suina; Suidae; Sus.

COMMENT REFSEQ INFORMATION: The reference sequence is identical to

CM000812.4.

On Oct 11, 2011 this sequence version replaced gi:333795951.

Assembly Name: Sscrofa10.2

The genomic sequence for this RefSeq record is from the genome

assembly released by the Swine Genome Sequencing Consortium as

Sscrofa10.2 in August 2011 (see

/Projects/S_scrofa). Sscrofa10.2 is a mixed assembly of clones and contigs from the whole-genome shotgun

project AEMK00000000.1.

##Genome-Annotation-Data-START##

Annotation Provider :: NCBI

Annotation Status :: Full annotation

Annotation Version :: Sus scrofa Annotation Release 104

Annotation Pipeline :: NCBI eukaryotic genome annotation

pipeline

Annotation Software Version :: 5.1

Annotation Method :: Best-placed RefSeq; Gnomon

Features Annotated :: Gene; mRNA; CDS; ncRNA

##Genome-Annotation-Data-END##

FEATURES Location/Qualifiers

source 1..2265

/organism="Sus scrofa"

/mol_type="genomic DNA"

/db_xref="taxon:9823"

/chromosome="1"

/breed="mixed"

gene 1..2265

/gene="MC4R"

/note="melanocortin 4 receptor; Derived by automated

computational analysis using gene prediction method:

BestRefSeq."

/db_xref="GeneID:397359"

mRNA join(1..681,834..2265)

/gene="MC4R"

/product="melanocortin 4 receptor"

/inference="similar to RNA sequence, mRNA (same

species):RefSeq:NM_214173.1"

/exception="annotated by transcript or proteomic data"

/note="The RefSeq transcript has 2 indels compared to this genomic sequence; Derived by automated computational

analysis using gene prediction method: BestRefSeq."

/transcript_id="NM_214173.1"

/db_xref="GI:55741558"

/db_xref="GeneID:397359"

CDS join(534..681,834..1685)

/gene="MC4R"

/inference="similar to AA sequence (same

species):RefSeq:NP_999338.1"

/exception="annotated by transcript or proteomic data"

/note="The RefSeq protein has 1 indel compared to this

genomic sequence; Derived by automated computational