Working with NCBI
This chapter contains a manual on working with NCBI's databases using Python, Bash and R.
Instruction
Note
Before working with NCBI using Python or R languages user must call the library and set the email.
Do not forget to change the example@example.com to your actuall email address!
Step 1: Find articles in PubMed for a query of interest to you and return abstracts of those articles in plain text format
Input
Output
{'Count': '3', 'RetMax': '3', 'RetStart': '0', 'IdList': ['29097323', '19041262', '18819019'], 'TranslationSet': [{'From': 'Cyclophilin A', 'To': '"cyclophilin a"[MeSH Terms] OR "cyclophilin a"[All Fields]'}, {'From': 'Open reading frame', 'To': '"open reading frames"[MeSH Terms] OR ("open"[All Fields] AND "reading"[All Fields] AND "frames"[All Fields]) OR "open reading frames"[All Fields] OR ("open"[All Fields] AND "reading"[All Fields] AND "frame"[All Fields]) OR "open reading frame"[All Fields]'}, {'From': 'Real-time PCR', 'To': '"real-time polymerase chain reaction"[MeSH Terms] OR ("real-time"[All Fields] AND "polymerase"[All Fields] AND "chain"[All Fields] AND "reaction"[All Fields]) OR "real-time polymerase chain reaction"[All Fields] OR ("real"[All Fields] AND "time"[All Fields] AND "pcr"[All Fields]) OR "real time pcr"[All Fields]'}], 'QueryTranslation': '("cyclophilin a"[MeSH Terms] OR "cyclophilin a"[All Fields]) AND ("open reading frames"[MeSH Terms] OR ("open"[All Fields] AND "reading"[All Fields] AND "frames"[All Fields]) OR "open reading frames"[All Fields] OR ("open"[All Fields] AND "reading"[All Fields] AND "frame"[All Fields]) OR "open reading frame"[All Fields]) AND ("real time polymerase chain reaction"[MeSH Terms] OR ("real time"[All Fields] AND "polymerase"[All Fields] AND "chain"[All Fields] AND "reaction"[All Fields]) OR "real time polymerase chain reaction"[All Fields] OR ("real"[All Fields] AND "time"[All Fields] AND "pcr"[All Fields]) OR "real time pcr"[All Fields])'}
1. Fish Shellfish Immunol. 2018 Jan;72:383-388. doi: 10.1016/j.fsi.2017.10.053.
Epub 2017 Oct 31.
Molecular identification and expression analysis of a novel cyclophilin a gene
in the red swamp crayfish, Procambarus clarkii.
Zhu J(1), Lin F(2), Li F(2), Wang Y(3).
Author information:
(1)College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China;
School of Life Sciences, RanHuzhou University, Huzhou, 313000, China.
(2)Zhejiang Institute of Freshwater Fisheries, Huzhou, 313001, China.
(3)College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
Electronic address: ywang@zju.edu.cn.
Cyclophilin A (Cyp A) is the main intracellular receptor of cyclosporin A (CsA)
belonging to the immunophilin family, which is known as an effective
immunosuppressive drug. This study aimed to gain insights into the structure and
biological function of cyclophilin A in the red swamp crayfish, Procambarus
clarkii (PcCypA). We cloned PcCypA by homology cloning and anchored polymerase
chain reaction (PCR), and assessed its mRNA and protein expression levels in
different tissues using quantitative real-time PCR and western blot analysis,
respectively. The full-length DNA contained a 5' untranslated region (UTR)
comprising 108 base pairs (bp), an open reading frame of 495 bp encoding a
polypeptide of 164 amino acids with an estimated molecular mass of 17.3 kDa, and
a 3' UTR of 281 bp including a significant poly(A) plus tail sequence. The
predicted amino acid sequence of PcCypA shared high identity with CypA in other
organisms. PcCypA transcripts were detected in the hepatopancreas, gill, heart,
muscle, testis, and ovary of crayfish, with the highest expression levels in the
heart. Western blot analysis found one 17-kDa band in all of the tissues
examined, except for the ovary. Molecular identification and expression analysis
of PcCypA will facilitate further studies of the immune defense mechanisms in
red swamp crayfish, and provide new insights into freshwater invertebrate
immunology.
Copyright © 2017 Elsevier Ltd. All rights reserved.
DOI: 10.1016/j.fsi.2017.10.053
PMID: 29097323 [Indexed for MEDLINE]
2. Fish Shellfish Immunol. 2009 Jan;26(1):115-21. doi: 10.1016/j.fsi.2008.03.022.
Epub 2008 Apr 7.
Molecular cloning and mRNA expression of cyclophilin A gene in black tiger
shrimp (Penaeus monodon).
Qiu L(1), Jiang S, Huang J, Wang W, Zhu C, Su T.
Author information:
(1)The South China Sea Fisheries Research Institute, Chinese Academy of Fishery
Sciences, Guangzhou, PR China.
The techniques of homology cloning and anchored PCR were used to clone the
cyclophilin A (CypA) gene from black tiger shrimp (Penaeus monodon). The
full-length cDNA of black tiger shrimp CypA (btsCypA) contained a 5'
untranslated region (UTR) of 81 bp, an ORF (open reading frame) of 495 bp
encoding a polypeptide of 164 amino acids with an estimated molecular mass of
17.68 kDa and a 3' UTR of 308 bp. The predicted amino acid sequence of btsCypA
shared high identity with CypA in other organisms. A quantitative reverse
transcriptase Real-Time PCR (qRT-PCR) assay was developed to assess the mRNA
expression of btsCypA in different tissues and the temporal expression of
btsCypA in the hepatopancreas challenged by lipopolyssacharide (LPS).
Higher-level mRNA expression of btsCypA was detected in the tissues of
hepatopancreas and blood. The expression of btsCypA in the hepatopancreas was up
regulated after stimulated by LPS. The results indicated that btsCypA was a
constitutive and inducible expressed protein and could be induced by LPS.
DOI: 10.1016/j.fsi.2008.03.022
PMID: 19041262 [Indexed for MEDLINE]
1. Fish Shellfish Immunol. 2018 Jan;72:383-388. doi: 10.1016/j.fsi.2017.10.053.
Epub 2017 Oct 31.
Molecular identification and expression analysis of a novel cyclophilin a gene
in the red swamp crayfish, Procambarus clarkii.
Zhu J(1), Lin F(2), Li F(2), Wang Y(3).
Author information:
(1)College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China;
School of Life Sciences, RanHuzhou University, Huzhou, 313000, China.
(2)Zhejiang Institute of Freshwater Fisheries, Huzhou, 313001, China.
(3)College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
Electronic address: ywang@zju.edu.cn.
Cyclophilin A (Cyp A) is the main intracellular receptor of cyclosporin A (CsA)
belonging to the immunophilin family, which is known as an effective
immunosuppressive drug. This study aimed to gain insights into the structure and
biological function of cyclophilin A in the red swamp crayfish, Procambarus
clarkii (PcCypA). We cloned PcCypA by homology cloning and anchored polymerase
chain reaction (PCR), and assessed its mRNA and protein expression levels in
different tissues using quantitative real-time PCR and western blot analysis,
respectively. The full-length DNA contained a 5' untranslated region (UTR)
comprising 108 base pairs (bp), an open reading frame of 495 bp encoding a
polypeptide of 164 amino acids with an estimated molecular mass of 17.3 kDa, and
a 3' UTR of 281 bp including a significant poly(A) plus tail sequence. The
predicted amino acid sequence of PcCypA shared high identity with CypA in other
organisms. PcCypA transcripts were detected in the hepatopancreas, gill, heart,
muscle, testis, and ovary of crayfish, with the highest expression levels in the
heart. Western blot analysis found one 17-kDa band in all of the tissues
examined, except for the ovary. Molecular identification and expression analysis
of PcCypA will facilitate further studies of the immune defense mechanisms in
red swamp crayfish, and provide new insights into freshwater invertebrate
immunology.
Copyright © 2017 Elsevier Ltd. All rights reserved.
DOI: 10.1016/j.fsi.2017.10.053
PMID: 29097323 [Indexed for MEDLINE]
2. Fish Shellfish Immunol. 2009 Jan;26(1):115-21. doi: 10.1016/j.fsi.2008.03.022.
Epub 2008 Apr 7.
Molecular cloning and mRNA expression of cyclophilin A gene in black tiger
shrimp (Penaeus monodon).
Qiu L(1), Jiang S, Huang J, Wang W, Zhu C, Su T.
Author information:
(1)The South China Sea Fisheries Research Institute, Chinese Academy of Fishery
Sciences, Guangzhou, PR China.
The techniques of homology cloning and anchored PCR were used to clone the
cyclophilin A (CypA) gene from black tiger shrimp (Penaeus monodon). The
full-length cDNA of black tiger shrimp CypA (btsCypA) contained a 5'
untranslated region (UTR) of 81 bp, an ORF (open reading frame) of 495 bp
encoding a polypeptide of 164 amino acids with an estimated molecular mass of
17.68 kDa and a 3' UTR of 308 bp. The predicted amino acid sequence of btsCypA
shared high identity with CypA in other organisms. A quantitative reverse
transcriptase Real-Time PCR (qRT-PCR) assay was developed to assess the mRNA
expression of btsCypA in different tissues and the temporal expression of
btsCypA in the hepatopancreas challenged by lipopolyssacharide (LPS).
Higher-level mRNA expression of btsCypA was detected in the tissues of
hepatopancreas and blood. The expression of btsCypA in the hepatopancreas was up
regulated after stimulated by LPS. The results indicated that btsCypA was a
constitutive and inducible expressed protein and could be induced by LPS.
DOI: 10.1016/j.fsi.2008.03.022
PMID: 19041262 [Indexed for MEDLINE]
3. Mol Biol Rep. 2009 Jul;36(6):1637-45. doi: 10.1007/s11033-008-9363-8. Epub
2008 Sep 26.
A cyclophilin A inducible expressed in gonad of zhikong scallop Chlamys farreri.
Song X(1), Wang L, Song L, Zhao J, Zhang H, Zheng P, Qiu L, Liu X, Wu L.
Author information:
(1)College of Animal Science and Technology, Northwest A&F University, Yangling,
Shaanxi, 712100, China.
Cyclophilin A (CypA), a receptor for the immunosuppressive agent cyclosporin A
(CsA), is a cis-trans peptidyl-prolyl isomerase (PPIase) which accelerates the
cis-trans isomerization of prolyl-peptide bonds, interacts with a variety of
proteins and therefore regulates their activities. One CypA (designated CfCypA)
cDNA was cloned from Chlamys farreri by expressed sequence tag (EST) and rapid
amplification of cDNA ends (RACE) techniques. The full-length cDNA of CfCypA
consisted of 1,248 nucleotides with a canonical polyadenylation signal sequence
AATAAA, a poly (A) tail, and an open reading frame (ORF) of 495 nucleotides
encoding a polypeptide of 164 amino acids. The deduced amino acid sequence
shared high similarity with CypA from the other species, indicating that CfCypA
should be a new member of the CypA family. Quantitative real-time (RT) PCR was
employed to assess the mRNA expression of CfCypA in various tissues and its
temporal expression in haemocytes and gonad of scallops challenged with Vibrio
anguillarum. The mRNA transcripts of CfCypA could be detected in all the
examined tissues with highest expression level in gonad. After bacterial
challenge, the expression level of CfCypA was almost unchanged in haemocytes,
but up-regulated in gonad and increased to the peak (22.59-fold; P < 0.05) at 4
h post-injection, and then dropped to the original level at 8 h post-injection.
These results indicated that CfCypA was constitutive expressed in haemocytes,
but could be induced in gonad, and perhaps played a critical role in response to
the bacterial challenge in gonad.
DOI: 10.1007/s11033-008-9363-8
PMID: 18819019 [Indexed for MEDLINE]
## Object of class 'efetch'
## 1. Fish Shellfish Immunol. 2018 Jan;72:383-388. doi: 10.1016/j.fsi.2017.10.053.
## Epub 2017 Oct 31.
##
## Molecular identification and expression analysis of a novel cyclophilin a gene
## in the red swamp crayfish, Procambarus clarkii.
##
## Zhu J(1), Lin F(2), Li F(2), Wang Y(3).
##
## Author information:
## (1)College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China;
## School of Life Sciences, RanHuzhou University, Huzhou, 313000, China.
## (2)Zhejiang Institute of Freshwater Fisheries, Huzhou, 313001, China.
## ...
## EFetch query using the 'pubmed' database.
## Query url: 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?=efe...'
## Retrieval type: 'abstract', retrieval mode: 'text'
Step 2: Find organism ID by name in the taxonomy database
Input
Output
Step 3: Query the nucleotide sequence database by gene name and return a table with UIDs
Input
handle = Entrez.esearch(db="nucleotide", term="cyclophilin AND Procambarus clarkii[orgn]")
record = Entrez.read(handle)
for rec in record["IdList"]:
temphandle = Entrez.read(Entrez.esummary(db="nucleotide", id=rec, retmode="text"))
print(temphandle[0]['Id']+"\t"+temphandle[0]['Caption']+"\t"+str(int(temphandle[0]['Length'])))#+"\n")
Output
Step 4: Give the nucleotide or protein sequence database a text query and then return the sequences in fasta format, which we write to a file
Input
handle = Entrez.esearch(db="protein", term="cyclophilin AND Procambarus clarkii[orgn]")
record = Entrez.read(handle)
Entrez.efetch(db="protein", id=record["IdList"], retmode="text", rettype="fasta").read()
with open("cyclophilin.fasta", "w") as ouf:
for rec in record["IdList"]:
lne = Entrez.efetch(db="protein", id=rec, retmode="text", rettype="fasta").read()
ouf.write(lne+"\n")
with open("cyclophilin.fasta", "r") as fastaf:
snippet = [next(fastaf) for x in range(5)]
print(snippet)
Output
>QPM92673.1 cyclophilin [Procambarus clarkii]
MKALVAVVALLVIFSVFNRADGQAGESKGPKVTHKVFFDITIGGVPKGTVVIGLFGSTVPRTAQNFFELA
QKPVGEGYKGSVFHRVIKDFMIQGGDFTRGDGTGGRSIYGERFADENFKLKHFGAGWLSMANAGKDTNGS
QFFITTNKTTWLDGKHVVFGKVLAGMPIIREIEASATDGRDRPVAEVKIVDSRGEALSQPFESVAKEDAT
D
>AGA16578.1 cyclophilin A [Procambarus clarkii]
MGNPQVFFDITANGKPLGRIVMELRADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPNFMCQGGDFTAG
NGTGGKSIYGSKFADENFQLPHDGPGILSMANAGPNTNGSQFFLCTVRTNWLDGKHVVLGKVTEGMDVVR
QIEGYGKPSGETSAKIVVANCGQL
## [1] ">QPM92673.1 cyclophilin [Procambarus clarkii]"
## [2] "MKALVAVVALLVIFSVFNRADGQAGESKGPKVTHKVFFDITIGGVPKGTVVIGLFGSTVPRTAQNFFELA"
## [3] "QKPVGEGYKGSVFHRVIKDFMIQGGDFTRGDGTGGRSIYGERFADENFKLKHFGAGWLSMANAGKDTNGS"
## [4] "QFFITTNKTTWLDGKHVVFGKVLAGMPIIREIEASATDGRDRPVAEVKIVDSRGEALSQPFESVAKEDAT"
## [5] "D"
## [6] ""
Step 5: Download the protein corresponding to the known nucleotide UID
Input
lhandle = Entrez.elink(dbfrom="nucleotide", db="protein", id="429843488")
lrecord = Entrez.read(lhandle)
prothandle = lrecord[0]["LinkSetDb"][0]['Link'][0]['Id']
rrecord = Entrez.efetch(db="protein", id=prothandle, rettype="fasta", retmode="text")
with open ("prot_from_nt.fasta", "w") as ouf:
ouf.write(rrecord.read()+"\n")
with open("prot_from_nt.fasta", "r") as fastaf:
snippet = [next(fastaf) for x in range(5)]
print(snippet)
Output
Step 6: Download all sequences from the PMID ... job and write them to a fasta file
Input
lhandle = Entrez.elink(dbfrom="pubmed", db="nucleotide", id="19041262")
lrecord = Entrez.read(lhandle)
ids = []
for el in lrecord[0]["LinkSetDb"][0]["Link"]:
ids.append(el['Id'])
rrecord = Entrez.efetch(db="nucleotide", id=ids[:4], rettype="fasta", retmode="text")
with open ("py_fasta_pmid.fasta", "w") as ouf:
ouf.write(rrecord.read()+"\n")
with open("py_fasta_pmid.fasta", "r") as fastaf:
snippet = [next(fastaf) for x in range(5)]
print(snippet)
ms2 <- esearch(term = "Cyclophilin A AND Open reading frame AND Real-time PCR", db = "pubmed")
lnk <- elink(ms2[2], dbFrom = "pubmed", dbTo = "nuccore")
f2 <- efetch(lnk, rettype = "fasta", retmode = "text")
write(content(f2), "py_fasta_pmid_R.fa")
read_seq <- readLines("py_fasta_pmid_R.fa")
head(read_seq)
Output
['>EU164775.1 Penaeus monodon cyclophilin A mRNA, complete cds\n', 'CTCGTCCTCGGTTCCCGGCGATCCTCTGGAGATTGTTGCCGTAGATGGACTTGCGAGCAGACCTACACCA\n', 'ACTTAGCCACCATGGGCAACCCCAAAGTCTTTTTCGACATTACCGCTGACAACCAGCCCGTTGGCAGGAT\n', 'CGTCATGGAGCTCCGCGCCGACGTGGTCCCCAAGACCGCCGAGAACTTCCGGTCGCTGTGCACGGGCGAG\n', 'AAGGGCTTCGGCTACAAGGGTTCCTGCTTCCACCGCGTGATCCCCAACTTCATGTGTCAGGGAGGCGACT\n']
>EU164775.1 Penaeus monodon cyclophilin A mRNA, complete cds
CTCGTCCTCGGTTCCCGGCGATCCTCTGGAGATTGTTGCCGTAGATGGACTTGCGAGCAGACCTACACCA
ACTTAGCCACCATGGGCAACCCCAAAGTCTTTTTCGACATTACCGCTGACAACCAGCCCGTTGGCAGGAT
CGTCATGGAGCTCCGCGCCGACGTGGTCCCCAAGACCGCCGAGAACTTCCGGTCGCTGTGCACGGGCGAG
AAGGGCTTCGGCTACAAGGGTTCCTGCTTCCACCGCGTGATCCCCAACTTCATGTGTCAGGGAGGCGACT
TCACCGCCGGCAACGGCACGGGCGGCAAGTCCATCTACGGCAACAAATTCGAGGACGAGAACTTCGCACT
GAAGCACACCGGCCCCGGCACCCTGTCCATGGCCAACGCCGGCCCCAACACCAACGGGTCGCAATTCTTC
ATCTGCACCGTCAAAACCCCCTGGCTGGACAACAAGCACGTGGTTTTCGGCTCCGTGGTGGAGGGCATGG
ACATCGTGCGCCAGGTCGAGGGTTTCGGCACCCCCAACGGCTCTTGCAAGCGGAAAGTGATGATCGCCAA
CTGCGGCCAGCTGTAAAGTTTCAGAACATTCCCCCTTAGCCGCCCACCCCTTTTTTTTTTGATGTAATTG
## [1] ">EU164775.1 Penaeus monodon cyclophilin A mRNA, complete cds"
## [2] "CTCGTCCTCGGTTCCCGGCGATCCTCTGGAGATTGTTGCCGTAGATGGACTTGCGAGCAGACCTACACCA"
## [3] "ACTTAGCCACCATGGGCAACCCCAAAGTCTTTTTCGACATTACCGCTGACAACCAGCCCGTTGGCAGGAT"
## [4] "CGTCATGGAGCTCCGCGCCGACGTGGTCCCCAAGACCGCCGAGAACTTCCGGTCGCTGTGCACGGGCGAG"
## [5] "AAGGGCTTCGGCTACAAGGGTTCCTGCTTCCACCGCGTGATCCCCAACTTCATGTGTCAGGGAGGCGACT"
## [6] "TCACCGCCGGCAACGGCACGGGCGGCAAGTCCATCTACGGCAACAAATTCGAGGACGAGAACTTCGCACT"