Using EUtils
I've been working on an updated client library in Python for
NCBI's EUtils.
It's still in alpha mode. I'm getting it in ship-shape so a couple
of my students can
present
it.
Here are some example of it in action.
Load the EUtils library
>>> import EUtils
# list all the databases served by EUtils
>>> dbs = EUtils.dblist()
>>> dbs
['pubmed', 'protein', 'nucleotide', 'structure', 'genome', 'books',
'cancerchromosomes', 'cdd', 'domains', 'gene', 'genomeprj', 'gensat',
'geo', 'gds', 'homologene', 'journals', 'mesh', 'ncbisearch',
'nlmcatalog', 'omia', 'omim', 'pmc', 'popset', 'probe', 'pcassay',
'pccompound', 'pcsubstance', 'snp', 'taxonomy', 'unigene', 'unists']
>>>
# Information about searching PubMed
>>> dbinfo = EUtils.dbinfo("pubmed")
# database name
>>> dbinfo.db
'pubmed'
# name to display in a menu
>>> dbinfo.menu_name
'PubMed'
# short description
>>> dbinfo.description
'PubMed bibliographic record'
# the last time it was updated
>>> dbinfo.last_update
datetime.datetime(2005, 9, 30, 6, 16)
# number of records in the database
>>> dbinfo.count
15830150
# List of searchable fields
>>> for field in dbinfo.field_list:
... print field.name + ": " + field.description
...
ALL: All terms from all searchable fields
UID: Unique number assigned to publication
FILT: Limits the records
TITL: Words in title of publication
WORD: Free text associated with publication
MESH: Medical Subject Headings assigned to publication
MAJR: MeSH terms of major importance to publication
AUTH: Author(s) of publication
JOUR: Journal abbreviation of publication
AFFL: Author's institutional affiliation and address
ECNO: EC number for enzyme or CAS registry number
SUBS: CAS chemical name or MEDLINE Substance Name
PDAT: Date of publication
EDAT: Date publication first accessible through Entrez
VOL: Volume number of publication
PAGE: Page number(s) of publication
PTYP: Type of publication (e.g., review)
LANG: Language of publication
ISS: Issue number of publication
SUBH: Additional specificity for MeSH term
SI: Cross-reference from publication to other databases
MHDA: Date publication was indexed with MeSH terms
TIAB: Free text associated with Abstract/Title
OTRM: Other terms associated with publication
INVR: Investigator
COLN: Corporate Author of publication
CNTY: Country of publication
PAPX: MeSH pharmacological action pre-explosions
GRNT: NIH Grant Numbers
MDAT: Date of last modification
CDAT: Date of completion
PID: Publisher ID
FAUT: First Author of publication
FULL: Full Author Name(s) of publication
>>>
# The information about a field
>>> all_field = dbinfo.field_list[0]
>>> all_field.name, all_field.description, all_field.term_count
('ALL', 'All terms from all searchable fields', 51491726)
>>> all_field.is_date, all_field.is_numerical, all_field.single_token, \
... all_field.hierarchy
(False, False, False, False)
>>>
I can search; by default it searchs PubMed. I'll search for two
papers I wrote some years back.
>>> results = EUtils.search("dalke AND vmd")
>>> results
<EUtils.HistoryClient.LiteratureRecordSet object at 0x102abb0>
>>> len(results)
2
>>>
I can get the database identifiers (this does an efetch of uilist
under the covers)
>>> results.dbids
DBIds('pubmed', ['9390282', '8744570'])
>>>
The e* methods are the low-level requests for a given format. They
return file handles. I'll get the two records in medline format.
>>> f = results.efetch("medline")
>>> print f.read()
PMID- 9390282
OWN - NLM
STAT- MEDLINE
DA - 19980115
DCOM- 19980115
LR - 20041117
PUBM- Print
DP - 1997
TI - Using Tcl for molecular visualization and analysis.
PG - 85-96
AB - Reading and manipulating molecular structure data is a standard task in
every molecular visualization and analysis program, but is rarely
available in a form readily accessible to the user. Instead, the
development of new methods for analysis, display, and interaction is often
achieved by writing a new program, rather than building on pre-existing
software. We present the Tcl-based script language used in our molecular
modeling program, VMD, and show how it can access information about the
molecular structure, perform analysis, and graphically display and animate
the results. The commands are available to the user and make VMD a useful
environment for studying biomolecules.
AD - Beckman Institute, Urbana, IL 61801, USA.
FAU - Dalke, A
AU - Dalke A
FAU - Schulten, K
AU - Schulten K
LA - eng
GR - 5 P41 RR05969-04/RR/NCRR
PT - Journal Article
PL - SINGAPORE
TA - Pac Symp Biocomput
JID - 9711271
RN - 0 (Proteins)
RN - 9007-49-2 (DNA)
SB - IM
MH - *Computer Simulation
MH - DNA/*chemistry
MH - Databases, Factual
MH - *Models, Molecular
MH - Nucleic Acid Conformation
MH - *Programming Languages
MH - Protein Conformation
MH - Protein Structure, Secondary
MH - Proteins/*chemistry
MH - Research Support, U.S. Gov't, Non-P.H.S.
MH - Research Support, U.S. Gov't, P.H.S.
EDAT- 1997/12/09
MHDA- 1997/12/09 00:01
PST - ppublish
SO - Pac Symp Biocomput 1997;:85-96.
PMID- 8744570
OWN - NLM
STAT- MEDLINE
DA - 19961204
DCOM- 19961204
LR - 20041117
PUBM- Print
IS - 0263-7855
VI - 14
IP - 1
DP - 1996 Feb
TI - VMD: visual molecular dynamics.
PG - 33-8, 27-8
AB - VMD is a molecular graphics program designed for the display and analysis
of molecular assemblies, in particular biopolymers such as proteins and
nucleic acids. VMD can simultaneously display any number of structures
using a wide variety of rendering styles and coloring methods. Molecules
are displayed as one or more "representations," in which each
representation embodies a particular rendering method and coloring scheme
for a selected subset of atoms. The atoms displayed in each representation
are chosen using an extensive atom selection syntax, which includes
Boolean operators and regular expressions. VMD provides a complete
graphical user interface for program control, as well as a text interface
using the Tcl embeddable parser to allow for complex scripts with variable
substitution, control loops, and function calls. Full session logging is
supported, which produces a VMD command script for later playback.
High-resolution raster images of displayed molecules may be produced by
generating input scripts for use by a number of photorealistic
image-rendering applications. VMD has also been expressly designed with
the ability to animate molecular dynamics (MD) simulation trajectories,
imported either from files or from a direct connection to a running MD
simulation. VMD is the visualization component of MDScope, a set of tools
for interactive problem solving in structural biology, which also includes
the parallel MD program NAMD, and the MDCOMM software used to connect the
visualization and simulation programs. VMD is written in C++, using an
object-oriented design; the program, including source code and extensive
documentation, is freely available via anonymous ftp and through the World
Wide Web.
AD - Theoretical Biophysics Group, University of Illinois, Urbana 61801, USA.
FAU - Humphrey, W
AU - Humphrey W
FAU - Dalke, A
AU - Dalke A
FAU - Schulten, K
AU - Schulten K
LA - eng
GR - 5 P41 RR05969-04/RR/NCRR
PT - Journal Article
PL - UNITED STATES
TA - J Mol Graph
JID - 9014762
RN - 0 (Nucleic Acids)
RN - 0 (Proteins)
SB - IM
MH - *Computer Graphics
MH - *Computer Simulation
MH - Computers
MH - *Models, Molecular
MH - Nucleic Acids/chemistry
MH - Proteins/chemistry
MH - Research Support, Non-U.S. Gov't
MH - Research Support, U.S. Gov't, Non-P.H.S.
MH - Research Support, U.S. Gov't, P.H.S.
MH - User-Computer Interface
EDAT- 1996/02/01
MHDA- 1996/02/01 00:01
AID - 0263785596000185 [pii]
PST - ppublish
SO - J Mol Graph 1996 Feb;14(1):33-8, 27-8.
The methods without the 'e' prefix provide a higher-level interface by
parsing the request. 'Fetch' on a literature database does an efetch
of the XML format and processes the records using
ElementTree, which
is included with my EUtils package. (Should it be included? Should it
use an existing ElementTree/cElementTree if it exists? Should split
the result into multiple ElementTrees or change it to return a single
ElementTree? Hmmm....)
>>> trees = results.fetch()
>>> trees
[<Element PubmedArticle at 29a8df0>, <Element PubmedArticle at 29b5198>]
>>> trees[0].find(".//ArticleTitle").text
'Using Tcl for molecular visualization and analysis.'
>>>
In the previous case the
XPath expression
".//ArticleTitle" means "find any element with tag "ArticleTitle".
The EUtils search string is the Entrez search string. (Additional PubMed specific help.) It is quite powerful.
# Search for publications in 1997
>>> len(EUtils.search("dalke AND 1997[PDAT]"))
3
# Authors with name "J. Smith"; note the use of double quotes
>>> len(EUtils.search('"smith j"[AU]'))
2017
>>>
I'll search GenPept for bacteriorhodopsin records.
>>> proteins = EUtils.search("bacteriorhodopsin", "protein")
>>> len(proteins)
459
# That's a few too many; get the first 20 records
>>> proteins = proteins[:20]
>>> proteins
<EUtils.HistoryClient.SequenceRecordSet object at 0x29bac50>
>>> len(proteins)
20
# Fetch the 'summary' format for those 20 records
>>> print proteins.efetch("summary").read()
1: XP_712857
hypothetical protein CaO19.12001 [Candida albicans SC5314]
gi|68486496|ref|XP_712857.1|[68486496]
2: XP_712951
hypothetical protein CaO19.4526 [Candida albicans SC5314]
gi|68486305|ref|XP_712951.1|[68486305]
3: XP_713724
hypothetical protein CaO19.11148 [Candida albicans SC5314]
gi|68484666|ref|XP_713724.1|[68484666]
4: XP_713758
hypothetical protein CaO19.3664 [Candida albicans SC5314]
gi|68484597|ref|XP_713758.1|[68484597]
5: XP_660965
hypothetical protein AN3361.2 [Aspergillus nidulans FGSC A4]
gi|67525807|ref|XP_660965.1|[67525807]
6: P69052
Archaerhodopsin 1 precursor (AR 1) (Bacterio-opsin)
gi|60391839|sp|P69052|BACR1_HALSS[60391839]
7: P69051
Archaerhodopsin 1 precursor (AR 1)
gi|60391838|sp|P69051|BACR1_HALS1[60391838]
8: XP_448732
unnamed protein product [Candida glabrata]
gi|50292599|ref|XP_448732.1|[50292599]
9: XP_448541
unnamed protein product [Candida glabrata]
gi|50292217|ref|XP_448541.1|[50292217]
10: XP_447235
unnamed protein product [Candida glabrata]
gi|50289607|ref|XP_447235.1|[50289607]
11: Q9HPU8
Putative bacterio-opsin activator
gi|47115564|sp|Q9HPU8|BAT_HALSA[47115564]
12: Q9F7P4
Green-light absorbing proteorhodopsin precursor (GPR)
gi|32699616|sp|Q9F7P4|PRRG_PRB01[32699616]
13: Q9AFF7
Blue-light absorbing proteorhodopsin precursor (BPR)
gi|32699602|sp|Q9AFF7|PRRB_PRB02[32699602]
14: O93743
Sensory rhodopsin (SR)
gi|14194476|sp|O93743|BACS_HALSD[14194476]
15: O93742
Halorhodopsin (HR)
gi|14194475|sp|O93742|BACH_HALSD[14194475]
16: O93741
Halorhodopsin (HR)
gi|14194474|sp|O93741|BACH_HALS4[14194474]
17: O93740
Bacteriorhodopsin (BR)
gi|14194473|sp|O93740|BACR_HALS4[14194473]
18: NP_010316
Protein that localizes primarily to the plasma membrane, also found at the
nuclear envelope; has similarity to Hsp30p and Yro2p, which are induced during
heat shock; Mrh1p [Saccharomyces cerevisiae]
gi|6320236|ref|NP_010316.1|[6320236]
19: NP_009950
Hydrophobic plasma membrane localized, stress-responsive protein that negatively
regulates the H(+)-ATPase Pma1p; induced by heat shock, ethanol treatment, weak
organic acid, glucose limitation, and entry into stationary phase; Hsp30p
[Saccharomyces cerevisiae]
gi|6319869|ref|NP_009950.1|[6319869]
20: NP_009610
Putative plasma membrane protein of unknown function, transcriptionally
regulated by Haa1p; green fluorescent protein (GFP)-fusion protein localizes to
the cell periphery and bud; Yro2p [Saccharomyces cerevisiae]
gi|6319528|ref|NP_009610.1|[6319528]
# Fetch the 'fasta' format for those 20 records
>>> print proteins.efetch("fasta").read()
>gi|68486496|ref|XP_712857.1| hypothetical protein CaO19.12001 [Candida albicans SC5314]
MSAAVSTLSDIIKRNDAVNVNPPNPIIDLHITEHGSDWLWAVFSVFALFAIVHGFIYSFTDVRKSGLKRA
LLTIPLFNSAVFAFAYYTYASNLGYTWILTEFNHAGTGFRQIFYAKFVAWFLGWPLVLAIFQIITNTSFT
TTEDESDLLKKFISLFEALFTRVLAIEVFVLGLLIGALIESTYKWGYFTFAVVFQLFAIYLVINDVVVSF
GSSSHSVFGNALILAFVIVWILYPVAWGLSEGGNVIQPDSEAVFYGILDLITFGVIPIILTWIAINNVDE
EFFTKIWHFHLKPENEHAPTATEDVEKAVGETPRHSGDTAVAPSGVPDTGVAQAQAEAEERI
>gi|68486305|ref|XP_712951.1| hypothetical protein CaO19.4526 [Candida albicans SC5314]
MSAAVSTLSDIIKRNDAVNVNPPNPIIDLHITEHGSDWLWAVFSVFALFAIVHGFIYSFTDVRKSGLKRA
LLTIPLFNSAVFAFAYYTYASNLGYTWILTEFNHAGTGFRQIFYAKFVAWFLGWPLVLAIFQIITNTSFT
TTEDESDLLKKFISLFEALFTRVLAIEVFVLGLLIGALIESTYKWGYFTFAVVFQLFAIYLVINDVVVSF
GSSSHSVFGNALILAFVIVWILYPVAWGLSEGGNVIQPDSEAVFYGILDLITFGVIPIILTWIAINNVDE
EFFTKIWHFHLKPENEHAPTATEDVEKAVGETPRHSGDTAVAPSGVPDTGVAQAQAEAEERI
>gi|68484666|ref|XP_713724.1| hypothetical protein CaO19.11148 [Candida albicans SC5314]
MAVASTFIHNNLEVMNRNTATKVNPTNSLVNMHITDHGSDWLWAAFSVFLLLTIIHLLLFLYGNFRKPGV
KNSLLVIPLFTNAVFSVFYFTYASNLGYAWQAVEFQHAGTGLRQIFYAKFVAWFVGWPAVLALFEIVTST
VLDRIEENPNIFKKFFLIFQTWLVKFIFVEIYVLGLLIGSIIFSTYKFGYFTFAVFFQLLLMVWVGRDLH
RSFKSPSHSNIANFFLIFFYLVWILYPVAWGLSEGGNVIQPDSEAVFYGILDLITFGLMPTILIFFAIKG
CDEEFFSKLWQYHVKSEAESIHENEKAVAETPSTEAGVVDAEVDNEPQAQV
>gi|68484597|ref|XP_713758.1| hypothetical protein CaO19.3664 [Candida albicans SC5314]
MAVASTFIHNNLEVMNRNTATKVNPTNSLVNMHITDHGSDWLWAAFSVFLLLTIIHLLLFLYGNFRKPGV
KNSLLVIPLFTNAVFSVFYFTYASNLGYAWQAVEFQHAGTGLRQIFYAKFVAWFVGWPAVLALFEIVTST
VLDRIEENPNIFKKFFLIFQTWLVKFIFVEIYVLGLLIGSIIFSTYKFGYFTFAVFFQLLLMVWVGRDLH
RSFKSPSHSNIANFFLIFFYLVWILYPVAWGLSEGGNVIQPDSEAVFYGILDLITFGLMPTILIFFAIKG
CDEEFFSKLWQYHVKSEAESIHENEKAVAETPSTEAGVVDAEVDNEPQAQV
>gi|67525807|ref|XP_660965.1| hypothetical protein AN3361.2 [Aspergillus nidulans FGSC A4]
MIEDALKKTVTVTQTLTETVTKAVPSHDPTSSWTTTTSVAPIPTVIPDHPTFQAVDTAAKRTLWVVTVLM
ALSSLVFYILSNRVQLPKRVIHYLVATATTVSFIIYLALATGQGMDWKYDTYNHKHKHVPDTEYGIVRQV
LWLRYVNWFLTGPLILASLTLLSGLPGASLFAAIVADWVMLGTGLFGTYAPNTSRKWIWFALSAIAFITL
IYHIGIKGTRAANNRDSHTRRLFSAIASVALLAKALYPITLAAGPLSLKLGLTGETILFAIHDIVIQGIL
GYWLVIANDAATGTNLYVDGFWSSGLGNEGAIRINEEEGA
>gi|60391839|sp|P69052|BACR1_HALSS Archaerhodopsin 1 precursor (AR 1) (Bacterio-opsin)
MDPIALTAAVGADLLGDGRPETLWLGIGTLLMLIGTFYFIVKGWGVTDKEAREYYSITILVPGIASAAYL
SMFFGIGLTEVQVGSEMLDIYYARYADWLFTTPLLLLDLALLAKVDRVSIGTLVGVDALMIVTGLVGALS
HTPLARYTWWLFSTICMIVVLYFLATSLRAAAKERGPEVASTFNTLTALVLVLWTAYPILWIIGTEGAGV
VGLGIETLLFMVLDVTAKVGFGFILLRSRAILGDTEAPEPSAGAEASAAD
>gi|60391838|sp|P69051|BACR1_HALS1 Archaerhodopsin 1 precursor (AR 1)
MDPIALTAAVGADLLGDGRPETLWLGIGTLLMLIGTFYFIVKGWGVTDKEAREYYSITILVPGIASAAYL
SMFFGIGLTEVQVGSEMLDIYYARYADWLFTTPLLLLDLALLAKVDRVSIGTLVGVDALMIVTGLVGALS
HTPLARYTWWLFSTICMIVVLYFLATSLRAAAKERGPEVASTFNTLTALVLVLWTAYPILWIIGTEGAGV
VGLGIETLLFMVLDVTAKVGFGFILLRSRAILGDTEAPEPSAGAEASAAD
>gi|50292599|ref|XP_448732.1| unnamed protein product [Candida glabrata]
MSYVDLYKRGGNEAVKINPPTGADFHITSRGSDWAWAVFCVMFFCAIVMVLLMFRKTANDRLAYYTAIAP
CVFMGIAYFTIASNLGWIPVRAKYNHVRTSTQQQHPGVRQIFYARYVGWFMALPWPVIQASLMGKTPIWQ
IAFNIAMTEVFTVCFLIAACVHSTYKWGYMTIGCGGAIVAMISVMTTTRHLVRAKKDGELWKGFNIYFGL
VMFFWAIYPICFGITDGGNVLQPDSALIFYGILDIILYAFLPCLWVPIASYIGISNMGYNFSDAEAGMTT
SNTMATVASPAMSPTPKTPKTPKTPATGKKAKKSMA
>gi|50292217|ref|XP_448541.1| unnamed protein product [Candida glabrata]
MVDIFTDVIQNKGGNRAISVNPPHDLDFHITKRGSDWLWAVFACFGLLMVVYIFLFFIAELKGSRITRYA
IAPAFLIAMFEFFGYFTYASNLGWTGVQAEFNHVTVDTPVTGLVPGVRQIFYSKFCAWFLSWPCLLFLIE
LAGIGTTLNPGEEISALDLIHSLLVQMTGTLYWVVALLVGALIHSTYKWGYFTFGAAAMLVVQGIQVRRQ
FFVLKTRGFTACLLILSMLIVWAYFICWGVSEGGNKIQPDSEAIFYGILDLCIFGILPAYLVFITNHYGL
WPSFKLTKSGEQEMYPEKVEDPESVRASGETAI
>gi|50289607|ref|XP_447235.1| unnamed protein product [Candida glabrata]
MSTFVDLYKRGGNEAVKINPPTGADFHITSRGSDWLWAAFCVFLLLAIVFVLLMFRKPVNNRFVYLTAIA
PNVFMAIAYFSIASNLGWIPVRAKYNHVRTSTQQQHPGVRQIFYARYVGWFMALPWPLIQASILGKTPVW
HVAFNCTMGCVFSVCFLIAACVHSTYKWGYFTIGCGAGIVSIISLMTTTYTLIKKCGDKEIKRCFLIYVC
PIIVLYLVAWPVCFGITDGGNVLQPDSEAIFYGIIDLLLLGIFPALYVPMASHVGYENITYGIFDSAIGG
AAPGGMAHSASMDIEKSPMSATSSPTPVSPTPKAGIKKPKLKLKK
>gi|47115564|sp|Q9HPU8|BAT_HALSA Putative bacterio-opsin activator
MTSVQNTESETAAGATTIGVLFAGSDPETGPAACDLDEDGRFDVTQIRDFVAARDRVDDPDIDCVVAVHE
PDGFDGVAFLEAVRQTHAEFPVVVVPTAVDEDVARRAVDADATGLVPAVSEDATAAIADRIEQSAPAHSE
DTETRMPISDLTVESERRLKEQALDEAPIGITISDATDPEEPIIYINDSFEDITGYSPDEVVGANHRFLQ
GPKTNEDRVAEFWTAITEDHDTQVVLRNYRRDGSLFWNQVDISPIYDEDGTVSHYVGFQMDVSERMAAQQ
ELQGERQSLDRLLDRVNGLMNDVTSALVRAADREEIETRITDRIGTGGEYAGAWFGRYDATEDTITVAEA
AGDCEGCDGDVFDLASAGEAVALLQDVVEQREALVSTDADGVSGTADGDACVLVPVTYRSTTYGVLAVST
AEHRIDDREQVLLRSLGRTTGASINDALTRRTIATDTVLNIGVELSDTALFLVELAGATDTTFEQEATIA
DSQTQGVLMLVTTPHDDPQAVVDTALGYDAVQDAEVIVSTDDESVVQFDLSSSPLVDVLSECGSRVIRMH
ADRTTLELDVRVGTEGAARRVLSTLRDKYADVELVAYHEDDPEQTPHGFREELRNDLTDRQLTALQKAYV
SGYFEWPRRAEGKQLAESMDIVPSTYHQHLQAAKQKLVGAFFEE
>gi|32699616|sp|Q9F7P4|PRRG_PRB01 Green-light absorbing proteorhodopsin precursor (GPR)
MKLLLILGSVIALPTFAAGGGDLDASDYTGVSFWLVTAALLASTVFFFVERDRVSAKWKTSLTVSGLVTG
IAFWHYMYMRGVWIETGDSPTVFRYIDWLLTVPLLICEFYLILAAATNVAGSLFKKLLVGSLVMLVFGYM
GEAGIMAAWPAFIIGCLAWVYMIYELWAGEGKSACNTASPAVQSAYNTMMYIIIFGWAIYPVGYFTGYLM
GDGGSALNLNLIYNLADFVNKILFGLIIWNVAVKESSNA
>gi|32699602|sp|Q9AFF7|PRRB_PRB02 Blue-light absorbing proteorhodopsin precursor (BPR)
MGKLLLILGSAIALPSFAAAGGDLDISDTVGVSFWLVTAGMLAATVFFFVERDQVSAKWKTSLTVSGLIT
GIAFWHYLYMRGVWIDTGDTPTVFRYIDWLLTVPLQVVEFYLILAACTSVAASLFKKLLAGSLVMLGAGF
AGEAGLAPVLPAFIIGMAGWLYMIYELYMGEGKAAVSTASPAVNSAYNAMMMIIVVGWAIYPAGYAAGYL
MGGEGVYASNLNLIYNLADFVNKILFGLIIWNVAVKESSNA
>gi|14194476|sp|O93743|BACS_HALSD Sensory rhodopsin (SR)
MTGAVTSAYWLAAVAFLIGVGITAALYAKLEGSRARTRLAALAVIPGFAGLSYVGMALGIGTVTVNGAEL
VGLRYVDWVVTTPLLVGFIGYNAGASRRAIAGVMIADALMIVFGAAAVVSGGTLKWALFGVSALFHVSLF
AYLYVIFPGGIPDDPMQRGLFSLLKNHVGLLWLAYPFVWLMGPAGIGFTGAVGAALTYAFLDVLAKVPYV
YFFYARRQAFIDVTDSRAAAKGDGPAVGGEAPVATGDDAPTAAD
>gi|14194475|sp|O93742|BACH_HALSD Halorhodopsin (HR)
MMETAADALASGTVPLEMTQTQIFEAIQGDTLLASSLWINIALAGLSILLFVYMGRNLEDPRAQLIFVAT
LMVPLVSISSYTGLVSGLTVSFLEMPAGHALAGQEVLTPWGRYLTWALSTPMILVALGLLAGSNATKLFT
AVTADIGMCVTGLAAALTTSSYLLRWVWYVISCAFFVVVLYVLLAEWAEDAEVAGTAEIFNTLKLLTVVL
WLGYPIFWALGAEGLAVLDVAVTSWAYSGMDIVAKYLFAFLLLRWVVDNERTVAGMAAGLGAPLARCAPA
DD
>gi|14194474|sp|O93741|BACH_HALS4 Halorhodopsin (HR)
MRSRTYHDQSVCGPYGSQRTDCDRDTDAGSDTDVHGAQVATQIRTDTLLHSSLWVNIALAGLSILVFLYM
ARTVRANRARLIVGATLMIPLVSLSSYLGLVTGLTAGPIEMPAAHALAGEDVLSQWGRYLTWTLSTPMIL
LALGWLAEVDTADLFVVIAADIGMCLTGLAAALTTSSYAFRWAFYLVSTAFFVVVLYALLAKWPTNAEAA
GTGDIFGTLRWLTVILWLGYPILWALGVEGFALVDSVGLTSWGYSLLDIGAKYLFAALLLRWVANNERTI
AVGQRSGRGAIGDPVED
>gi|14194473|sp|O93740|BACR_HALS4 Bacteriorhodopsin (BR)
MCCAALAPPMAATVGPESIWLWIGTIGMTLGTLYFVGRGRGVRDRKMQEFYIITIFITTIAAAMYFAMAT
GFGVTEVMVGDEALTIYWARYADWLFTTPLLLLDLSLLAGANRNTIATLIGLDVFMIGTGAIAALSSTPG
TRIAWWAISTGALLALLYVLVGTLSENARNRAPEVASLFGRLRNLVIALWFLYPVVWILGTEGTFGILPL
YWETAAFMVLDLSAKVGFGVILLQSRSVLERVATPTAAPT
>gi|6320236|ref|NP_010316.1| Protein that localizes primarily to the plasma membrane, also found at the nuclear envelope; has similarity to Hsp30p and Yro2p, which are induced during heat shock; Mrh1p [Saccharomyces cerevisiae]
MSTFETLIKRGGNEAIKINPPTGADFHITSRGSDWFWTCFCCYLLFGLILTFLMFRKPVNDRFFYLTGIA
PNFFMCIAYFTMASNLGWIPVKAKYNHVQTSTQKEHPGYRQIFYSRFVGWFLALPWPIIQICMLAGTPFW
QMAFNVCITEFFTVCWLIAACVHSTYKWGYYTIGLGAAIVVSISVMTTSYNLVKQRDNDIRLTFLVFFSI
IMFLWIIAYPTCFGITDGGNVLQPDSAGIFYGIIDLILMCFIPTLLVPIANHFGADKLGYHFGPSDAEAV
MAPKAPVASPRPAATPNLSKDKKKKSKKSKKSKKSKKSEE
>gi|6319869|ref|NP_009950.1| Hydrophobic plasma membrane localized, stress-responsive protein that negatively regulates the H(+)-ATPase Pma1p; induced by heat shock, ethanol treatment, weak organic acid, glucose limitation, and entry into stationary phase; Hsp30p [Saccharomyces cerevisiae]
MNDTLSSFLNRNEALGLNPPHGLDMHITKRGSDWLWAVFAVFGFILLCYVVMFFIAENKGSRLTRYALAP
AFLITFFEFFAFFTYASDLGWTGVQAEFNHVKVSKSITGEVPGIRQIFYSKYIAWFLSWPCLLFLIELAA
STTGENDDISALDMVHSLLIQIVGTLFWVVSLLVGSLIKSTYKWGYYTIGAVAMLVTQGVICQRQFFNLK
TRGFNALMLCTCMVIVWLYFICWGLSDGGNRIQPDGEAIFYGVLDLCVFAIYPCYLLIAVSRDGKLPRLS
LTGGFSHHHATDDVEDAAPETKEAVPESPRASGETAIHEPEPEAEQAVEDTA
>gi|6319528|ref|NP_009610.1| Putative plasma membrane protein of unknown function, transcriptionally regulated by Haa1p; green fluorescent protein (GFP)-fusion protein localizes to the cell periphery and bud; Yro2p [Saccharomyces cerevisiae]
MSDYVELLKRGGNEAIKINPPTGADFHITSRGSDWLFTVFCVNLLFGVILVPLMFRKPVKDRFVYYTAIA
PNLFMSIAYFTMASNLGWIPVRAKYNHVQTSTQKEHPGYRQIFYARYVGWFLAFPWPIIQMSLLGGTPLW
QIAFNVGMTEIFTVCWLIAACVHSTYKWGYYTIGIGAAIVVCISLMTTTFNLVKARGKDVSNVFITFMSV
IMFLWLIAYPTCFGITDGGNVLQPDSATIFYGIIDLLILSILPVLFMPLANYLGIERLGLIFDEEPAEHV
GPVAEKKMPSPASFKSSDSDSSIKEKLKLKKKHKKDKKKAKKAKKAKKAKKAQEEEEDVATDSE
Looks like I'm getting some yeast sequences too. I only want the ones
from halobacteria. That's done using the ORGN ("organism") field.
>>> proteins = EUtils.search( ... "bacteriorhodopsin AND halobacteria[ORGN]", "protein") >>> len(proteins) 224 >>>I can get the records in GenBank format, which I'll parse using Biopython. Here I'll show the gi and definition fields for each one. Err, since that's too long, how about the first 10?
>>> from Bio import GenBank
>>> for record in GenBank.Iterator(proteins[:10].efetch("genbank"),
... GenBank.RecordParser()):
... print record.gi, record.definition
...
60391839 Archaerhodopsin 1 precursor (AR 1) (Bacterio-opsin).
60391838 Archaerhodopsin 1 precursor (AR 1).
47115564 Putative bacterio-opsin activator.
14194476 Sensory rhodopsin (SR).
14194475 Halorhodopsin (HR).
14194474 Halorhodopsin (HR).
14194473 Bacteriorhodopsin (BR).
3023375 Archaerhodopsin 3 precursor (AR 3).
2829812 Cruxrhodopsin-3 (COP-3) (CR-3).
2829811 Cruxhalorhodopsin-3 precursor (CHR-3).
>>>
(If you fetch everything you'll find that Biopython doesn't handle one
of the records, which has a division of "ENV". I've added support for
that in the CVS version of Biopython.)
In doing this I noticed one of the records is
1633466 Crystal Structure Of Bacteriorhodopsin In Purple Membrane.I can get more information from it directly.
>>> dbids = EUtils.DBIds("protein", ["1633466"])
>>> print EUtils.efetch(dbids, "fasta").read()
>gi|1633466|pdb|2BRD| Crystal Structure Of Bacteriorhodopsin In Purple Membrane
XAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVP
FGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAI
STAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMV
LDVSAKVGFGLILLRSRAIFGEAEAPEPSADGAAATS
>>>
Okay, enough for now. Still need to talk about links, searches with
history, and a bit more.
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