Lab Worksheet 14 Solutions

The web interface to BLAST is available here: http://blast.ncbi.nlm.nih.gov/Blast.cgi

Let's search for proteins related to the following query sequence, which is the human chemokine receptor 4 (a receptor that plays a fundamental role in the immune system):

>human
MSIPLPLLQIYTSDNYTEEMGSGDYDSMKEPCFREENANFNKIFLPTIYSIIFLTGIVGN
GLVILVMGYQKKLRSMTDKYRLHLSVADLLFVITLPFWAVDAVANWYFGNFLCKAVHVIY
TVNLYSSVLILAFISLDRYLAIVHATNSQRPRKLLAEKVVYVGVWIPALLLTIPDFIFAN
VSEADDRYICDRFYPNDLWVVVFQFQHIMVGLILPGIVILSCYCIIISKLSHSKGHQKRK
ALKTTVILILAFFACWLPYYIGISIDSFILLEIIKQGCEFENTVHKWISITEALAFFHCC
LNPILYAFLGAKFKTSAQHALTSVSRGSSLKILSKGKRGGHSSVSTESESSSFHSS

Problems

Problem 1:

Download the blast results from the NCBI website in XML format and store them as cxcr4_BLAST.xml. Extract the genbank identifiers (written as gb|string|, where string is the actual identifier, consisting of letters, numbers, and the period symbol) for all matches with a score greater than or equal to 1600 and less than or equal 1800, and store them in a python list. For matches that list multiple genbank identifiers, only extract the first one.

In [1]:
from Bio.Blast import NCBIXML
import re

# open the downloaded file and parse with NCBIXML.read()
blast_handle = open("cxcr4_BLAST.xml")
blast_record = NCBIXML.read(blast_handle)
blast_handle.close()

gb_list = []
for alignment in blast_record.alignments:
    for hsp in alignment.hsps:
        if hsp.score >= 1600 and hsp.score <= 1800:
            match = re.search(r'gb\|([\w\d\.]+)\|', alignment.title)
            if match:
                gb_id = match.group(1)
                gb_list.append(gb_id)
                
print(gb_list)
['AAF89355.1', 'AAF89362.1', 'ABX55951.1', 'AAF42991.1', 'AAF42992.1', 'AAF42990.1', 'ABX55952.1', 'AAF37288.1', 'EFB23364.1', 'ABA28309.1', 'KFO22725.1', 'EHB03245.1', 'ELR58312.1', 'AAF89363.1', 'ACH54079.1', 'AAZ32767.1', 'AAF89359.1', 'AAC48852.1', 'ELK23194.1']

Problem 2:

Using the list of genbank identifiers obtained in the previous exercise, download the corresponding sequences from genbank and print them out in FASTA format.

Hints:

  • You will have to specify the database as "protein" for this to work, since the previous exercise generated identifiers for protein sequences.
  • Use the function SeqIO.write() to output your results in FASTA format, and use sys.stdout from the sys module as your output handle.
In [2]:
from Bio import Entrez, SeqIO
import sys

Entrez.email = "dariya.k.sydykova@gmail.com" # put your email here

handle = Entrez.efetch(db="protein", id=gb_list, rettype="gb", retmode="text")
records = SeqIO.parse(handle, "genbank")

for record in records:
    SeqIO.write(record, sys.stdout, "fasta")
    
handle.close() # important, close the handle only after you have iterated over the records. Otherwise you will get an error!
>AAF89355.1 chemokine receptor CXCR4, partial [Callithrix jacchus].
IYTSDNYTEEIGSGDYDSIKEPCFREENAHFNRIFLPTIYSIIFLTGIVGNGLVILVMGY
QKKLRSMTDKYRLHLSVADLLFVITLPFWAVDAVANWYFGKFLCKAVHVIYTVNLYSSVL
ILASISLDRYLAIVHATTSQRPPKLLAEKVVYVGVWIPALLLTIPDFIFANVSEADDRYI
CDRFYPNDLWVVVFQFQHIMVGLILPGIVILSCYCIIISKLSHSKGHQKRKALKTTVILI
LAFFACWLPYYIGISIDSFILLEIIRQGCEFENTVHKWISITEALAFFHCCLNPILYAFL
GAKFKTSAQHALTSVSRGSSLKILSKGKRGGHSSVSTESESSSFHSS
>AAF89362.1 chemokine receptor CXCR4, partial [Eulemur macaco].
IYTSDNYTEELGSGDYDSIKEPCFREENAHFNRIFLPTIYSIIFLTGIVGNGLVILVMGY
QKKLRSMTDKYRLHLSVADLLFVITLPFWAVDAVANWYFGKFLCKAVHVIYTVNLYSSVL
ILAFISLDRYLAIVHATNSQRPRKLSAEKVVYAGVWLPALLLTIPDFIFASVSEVDDRYI
CDRLYPNDLWVVVFQFQHIMVGLILPGIVILSCYCIIISKLSHSKGHQKRKALKTTVILI
LAFFACWLPYYIGISIDSFILLEIIKQGCEFENTVHKWISITEALAFFHCCLNPILYAFL
GAKFKTSAQHALSSVSRGSSLKILSKGKRGGHSSVSTESESSSFHSS
>ABX55951.1 chemokine receptor, partial [Oryctolagus cuniculus].
TSDNYTEELGSGDYDSIKEPCFREENAHFNRIFLPTIYSIIFLTGIVGNGLVILVMGYQK
KQRSMTDKYRLHLSVADLLFVITLPFWAVDAVANWYFGKFLCKAVHVIYTVNLYSSVLIL
AFISLDRYLAIVHATNSQKPRKLLAEKVVYVGVWIPALLLTIPDFIFANVREAEGRYICD
RFYPSDLWVVVFQFQHIMVGLILPGIVILSCYCIIISKLSHSKGHQKRKALKTTVILILA
FFACWLPYYIGISIDSFILLEIIKQGCEFENTVHKWISITEALAFFHCCLNPILYAFLGA
KFKTSAQHALTSVSRGSSLKILSKGKRGGHSSVSTESESSSFHSS
>AAF42991.1 CXC chemokine receptor 4, partial [Hylobates lar].
EEMGSGDYDSIKEPCFREENANFNKIFLPTIYSIIFLTGIVGNGLVILVMGYQEKLRSMT
DKYRLHLSVADLLFVITLPFWAVDAVANWYFGNFLCKAVHVIYTVNLYSSVLILAFISLD
RYLAIVHATNSQRPRKLLAEKVVYVGVWIPALLLTIPDFIFANVSEADDRYICDRFYPND
LWVVVFQFQHIMVGLILPGIVMLSCYCIIISKLSHSKGHQKRKALKTTVILILAFFACWL
PYYIGISIDSFILLEIIKQGCEFENTVHKWISITEALAFFHCCLNPILYAFLGAKFKTSA
QHALTSVSRGSSLKILSKGKRGGHSSVSTESESS
>AAF42992.1 CXC chemokine receptor 4, partial [Saguinus oedipus].
EEMGSGDYDSMKEPCFREENAHFNRIFLPTIYSIIFLTGIVGNGLVILVMGYQKKLRSMT
DKYRLHLSVADLLFVITLPFWAVDAVANWYFGKFLCKAVHVIYTVNLYSSVLILAFISLD
RYLAIVHATNSQRPRKLLAEKVVYVGVWIPALLLTIPDFIFANVSEADDRYICDRFYPND
LWVVVFQFQHIMVGLILPGIVILSCYCIIISKLSHFKGHQKRKALKTTVILILAFFACWL
PYYIGISIDSFILLEIIRQGCEFENTVHKWISITEALAFFHCCLNPILYAFLGAKFKTSA
QHALTSVSRGSSLKILSKGKRGGHSSVSTESESS
>AAF42990.1 CXC chemokine receptor 4, partial [Chlorocebus aethiops].
EEMGSGDYDSIKEPCFREENAHFNRIFLPTIYSIIFLTGIVGNGLVILVMGYQKKLRSMT
DKYRLHLSVADLLFVITLPFWAVDAVANWYFGNFLCKAVHVIYTVNLYSSVLILAFISLD
RYLAIVHATNSQRPRKLLAEKVVYVGVWIPALLLTIPHFIFASVSEADDRYICDRFYPND
LWVVVFQFQHIMVGLILPGIVILSCYCIIISKLSHSKGHQKRKALKTTVILILAFFACWL
PYYIGISIDSFILLEIIKQGCEFENTVHKWISITEALAFFHCCLNPILYAFLGAKFKTSA
QHALTSVSRGSSLKILSKGKRGGHSSVSTESESS
>ABX55952.1 chemokine receptor, partial [Oryctolagus cuniculus].
TSDNYTEELGSGDYDSIKEPCFREENAHFNRIFLPTIYSIIFLTGIVGNGLVILVMGYQK
KQRSMTDKYRLHLSVADLLFVITLPFWAVDAVANWYFGKFLCKAVHVIYTVNLYSSVLIL
AFISLDRYLAIVHATNSQKPRKLLAEKVVYVGVWIPALLLTIPDFIFANVREAEGRYICD
RFYPSDLWVVVFQFQHIMVGLILPGIVILSCYCIIISKLSHSKGHQKRKALKTTVILILA
FFACWLPYYIGISIDSFILLEIIKQGCEFENTVHKWISITEALAFFHCCLNPILYAFLGA
KFKTSAQHALTSVSRGSSLKILSKGKRGGHSSVSTESES
>AAF37288.1 CXCR4 receptor, partial [Saimiri boliviensis].
EEMGSGDYDSMKEPCFREENAHFNRIFLPTIYSIIFLTGIVGNGLVILVMGYQKKLRSMT
DKYRLHLSVADLLFVITLPFWAVDAVANWYFGKFLCKAVHVIYTVNLYSSVLILAFISLD
RYLAIVHATNSQRPRKLLAEKVVYVGVWIPALLLTIPDFIFANVSEADDRYICDRFYPND
LWVVVFQFQHIMVGLILPGIVILSCYCIIISKLSHSKGHQKRKALKTTVILILAFFACWL
PYYIGISIDSFILLEIIRQGCEFENTVHKWISITEALAFFHCCLNPILYAFLGAKFKTSA
QHALTSVSRRSNLKILSKGKRGGHSSVSTESESS
>EFB23364.1 hypothetical protein PANDA_017529, partial [Ailuropoda melanoleuca].
MSIPLPLLQIYPSDNYTEDDLGSGDYDSMKEPCFREENAHFNRIFLPTVYSIIFLTGIVG
NGLVILVMGYQKKLRSMTDKYRLHLSVADLLFVLTLPFWAVDAVANWYFGKFLCKAVHVI
YTVNLYSSVLILAFISLDRYLAIVHATNSQRPRKLLAEKVVYVGVWIPALLLTIPDFIFA
NVREADGRYICDRFYPNDSWLVVFQFQHIMVGLILPGIVILSCYCIIISKLSHSKGYQKR
KALKTTVILILAFFACWLPYYIGISIDSFILLEIIKQGCEFESTVHKWISITEALAFFHC
CLNPILYAFLGAKFKTSAQHALTSVSRGSSLKILSKGKRGGHSSVSTESESSSFHSS
>ABA28309.1 chemokine (C-X-C motif) receptor 4 [Canis lupus familiaris].
MEELHIYPSDNYTEEDLGSGDYDSMKEPCFREENAHFNRIFLPTVYSIIFLTGIVGNGLV
ILVMGYQKKLRSMTDKYRLHLSVADLLFVLTLPFWAVEAVANWYFGNFLCKAVHVIYTVN
LYSSVLILAFISLDRYLAIVHATNSQRPRKLLAEKVVYVGVWIPALLLTIPDFIFANVRE
ADDRYICDRFYPNDSWLVVFQFQHIMVGLILPGIVILSCYCIIISKLSHSKGYQKRKALK
TTVILILAFFACWLPYYIGISIDSFILLEIIKQGCEFEKTVHKWISITEALAFFHCCLNP
ILYAFLGAKFKTSAQHALTSVSRGSSLKILSKGKRGGHSSVSTESESSSFHSS
>KFO22725.1 C-X-C chemokine receptor type 4 [Fukomys damarensis].
MLLRAPPGTLFANNILCSLRKRRALRRPLLSSSDEIYTSDNYSEELGSGDYDSAKEPCFR
NENAHFNRIFLPTIYSIIFLTGIVGNGLVILVMGYQKKLRSMTDKYRLHLSVADLLFVIT
LPFWAVDAVANWYFGKFLCKAVHVIYTVNLYSSVLILAFISLDRYLAIVHATNSQRPRKL
LVEKAVYVGVWIPAVLLTIPDFIFANVIEGDGKFICDRFYPNDLWVVVFQFQHIMVGLIL
PGIVILSCYCIIISKLSHSKGHQKRKALKTTVILILAFFACWLPYYIGISIDSFILLEII
KQGCEFENTVHKWISITEALAFFHCCLNPILYAFLGAKFKTSAQHALTSVSRGSSLKILS
KGKRGGHSSVSTESESSSFHSS
>EHB03245.1 C-X-C chemokine receptor type 4 [Heterocephalus glaber].
MRHSEKLVLPAALQAHPALPKYWTRTSYWARDARRDQGCSSLAEASQGQHPSAPPLSPPP
LFGHSFTHPAFSSRPARAAHALLCERVFIKVWLRSETSICWLQQQIYTSDNYSEELGSGD
YDSAKEPCFRNENAHFNRIFLPTIYSIIFLTGIVGNGLVILVMGYQKKLRSMTDKYRLHL
SVADLLFVITLPFWAVDAVANWYFGKFLCKAVHVIYTVNLYSSVLILAFISLDRYLAIVH
ATNSQRPRKLLVERAVYVGVWIPAVLLTIPDFIFANVIEGEGKYICDRFYPNDLWVVVFQ
FQHIMVGLILPGIVILSCYCIIISKLSHSKGHQKRKALKTTVILILAFFACWLPYYIGIS
IDSFILLEIIKQGCEFENTVHKWISITEALAFFHCCLNPILYAFLGAKFKTSAQHALTSV
SRGSSLKILSKGKRGGHSSVSTESESSSFHSS
>ELR58312.1 C-X-C chemokine receptor type 4 [Bos mutus].
MSIPLPVFQIFTSDNYTEDDLGSGDYDSMKEPCFREENAHFNRIFLPTVYSIIFLTGIVG
NGLVILVMGYQKKLRSMTDKYRLHLSVADLLFVLTLPFWAVDAVANWYFGKFLCKAVHVI
YTVNLYSSVLILAFISLDRYLAIVHATNSQKPRKLLAEKVVYVGVWLPAVLLTIPDLIFA
DIKEVDERYICDRFYPSDLWLVVFQFQHIVVGLLLPGIVILSCYCIIISKLSHSKGYQKR
KALKTTVILILTFFACWLPYYIGISIDSFILLEIIQQGCEFESTVHKWISITEALAFFHC
CLNPILYAFLGAKFKTSAQHALTSVSRGSSLKILSKGKRGGHSSVSTESESSSFHSS
>AAF89363.1 chemokine receptor CXCR4, partial [Perodicticus potto].
IFTSDNYTEELGSGDYDSSKEPCFREENAHFNRIFLPTIYSIIFLTGIVGNGLVILVMGY
QKKLRSMTDKYRLHLSVADLLFVITLPFWAVDAVANWYFGEFLCKAVHVIYTVNLYSSVL
ILAFISLDRYLAIVHATNSQKPRKLLAEKVVYAGVWLPAFLLTIPDVIFASVREADNRYI
CDRFYPNDLWLAVFQFQHIMVGLILPGIVILSCYCIIISKLSHSKGHQKRKALKTTVILI
LAFFACWLPYYIGISIDSFILLEIIKQGCEFDNTVHKWISITEALAFFHCCLNPILYAFL
GAKFKTSAQHALTSVSRGSSLKILSKGKRGGHSSVSTESESSSFHSS
>ACH54079.1 chemokine receptor CXCR4 [Panthera leo].
MDGFRIYPSDNYTEDDLGSGDYDSMKEPCFREENAHFNRIFLPTVYSIIFLTGIVGNGLV
ILVMGYQKKLRSMTDKYRLHLSVADLLFVLTLPFWAVDAVANWYFGKFLCKAVHVIYTVN
LYSSVLILAFISLDRYLAIVHATNSQRPRKLLAEKVVYVGVWIPALLLTIPDFIFANVRE
ADGRYICDRFYPNDSWLVVFQFQHIMVGLILPGIVILSCYCIIISKLSHSKGYQKRKALK
TTVILILAFFACWLPYYIGISIDSFILLEIIKQGCEFESTVHKWISITEALAFFHCCLNP
ILYAFLGAKFKTSAQHALTSVSRGSSLKILSKGKRGGHSSVSTESESSSFHSS
>AAZ32767.1 CXCR4 [Sus scrofa].
MDGFRIFTSDNYTEDDLGSGDYDSIKEPCFREENAHFNRIFLPTVYSIIFLTGIVGNGLV
ILVMGYQKKLRSMTDKYRLHLSVADLLFVLTLPFWAVDAVANWYFGKFLCKAVHVIYTVN
LYSSVLILAFISLDRYLAIVHATNSQRPRKLLAEKVVYVGVWIPALLLTIPDFIFANVRE
GDGRYICDRFYPNDLWLVVFQFQHIMVGLILPGIVILSCYCIIISKLSHSKGYQKRKALK
TTVILILAFFACWLPYYIGISIDSFILLEIIQQGCEFESTVHKWISITEALAFFHCCLNP
ILYAFLGAKFKTSAQHALTSVSRGSSLKILSKGKRGGHSSVSTESESSSFHSS
>AAF89359.1 chemokine receptor CXCR4, partial [Nycticebus coucang].
IYTSDNYTEDLGSGDYDSMKEPCFREENAHFNRIFLPTIYSIIFLTGIVGNGLVILVMGY
QKKLRSMTDKYRLHLSVADLLFVITLPFWAVDAVANWYFGEFLCKAVHVIYTVNLYRSVL
ILAFISLDRYLAIVHATNSQRPRKLLAEKVVYAGVWLPAFLLTIPDVIFASVREADRYIC
DRFYPNDLWVVVFQFQHIMVGFILPGIVILSCYCIIISKLSHSKGHQKRKALKTTVILIL
AFFACWLPYYIGISIDSFILLEIIKQGCEFDNTVHKWISITEALAFFHCCLNPILYAFLG
AKFKTSAQHALTSVSRGSSLKILSKGKRGGHSSVSTESESSSFHSS
>AAC48852.1 CXCR-4 homolog [Felis catus].
MDGFRIYPSDNYTEDDLGSGDYDSMKEPCFREENAHFNRIFLPTVYSIIFLTGIVGNGLV
ILVMGYQKKLRSMTDKYRLHLSVADLLFVLTLPFWAVDAVANWYFGKFLCKAVHVIYTVN
LYSSVLILAFISLDRYLAIVHATNSQRPRKLLAEKVVYVGVWIPALLLTIPDFIFANVRE
ADGRYICDRFYPSDSWLVVFQFQHIMVGLILPGIVILSCYCIIISKLSHSKGYQKRKALK
TTVILILAFFACWLPYYIGISIDSFILLEIIKQGCEFESTVHKWISITEALAFFHCCLNP
ILYAFLGAKFKTSAQHALTSVSRGSSLKILSKGKRGGHSSVSTESESSSFHSS
>ELK23194.1 C-X-C chemokine receptor type 4 [Myotis davidii].
MDGFHIYPSDNYTEEDMGSGDYDSIKEPCFREENAHFNRIFLPTIYSIIFLTGIVGNGLV
ILVMGYQKKLRSMTDKYRLHLSVADLLFVLTLPFWAVDAVANWYFGKFLCKAVHVIYTVN
LYSSVLILAFISLDRYLAIVHATNSQRPRKLLAEKVVYVGVWIPALLLAIPDFIFANVRV
GEDRYICDRFYPNDVWMVVFQFQHIMVGLVLPGIVILSCYCIIISKLSHSKGYQKRKALK
TTVILILTFFACWLPYYIGLSIDSFILLEIIKQGCEFENTVHKWISITEALAFFHCCLNP
ILYAFLGAKFKSSAQHALTSVSRGSSLKILSKGKRGGHSSVSTESESSSFHSS

Problem 3:

Use the FASTA format of the sequences from problem 2 and make a multiple sequence alignment and a phylogenetic tree with the Clustal Omega web interface: http://www.ebi.ac.uk/Tools/msa/clustalo/.