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Index of PubCrawler results:


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:::::: Results for 'Picornaviruses' at PubMed
 
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No new records for 'Picornaviruses' today
MORE: 1-day-old records for 'Picornaviruses' (1)
MORE: 2-day-old records for 'Picornaviruses' (3)
MORE: 4-day-old records for 'Picornaviruses' (1)
MORE: 11-day-old records for 'Picornaviruses' (3)

:::::: Results for 'HCV' at PubMed
 
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No new records for 'HCV' today
MORE: 11-day-old records for 'HCV' (1)

:::::: Results for 'Miscellaneous' at PubMed
 
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No matching documents found in Entrez for the last 90 days

Database for this entry not updated. 		 

:::::: Results for 'Major journals' at PubMed
 
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34 hits after first visit for ' ( virus*[TITLE] OR virology[TITLE] ) AND ( Science[Journal Name] OR Nature*[Journal Name] OR 0027-8424[TA] OR Cell[TA] OR EMBO[TA] OR 0028-0836[TA] OR 1087-0156[TA] OR 1465-7392[TA] OR 1061-4036[TA] OR 1529-2908[TA] OR 1078-8956[TA] OR 1548-7091[TA] OR 1740-1526[TA] OR 1545-9993[TA] OR 1072-8368[TA] ) ' 		 

 Today's new results (1 item in total):

1:   Chesnokova LS, Nishimura SL, Hutt-Fletcher LM.   Related Articles
  Fusion of epithelial cells by Epstein-Barr virus proteins is triggered by binding of viral glycoproteins gHgL to integrins {alpha}v{beta}6 or {alpha}v{beta}8.
  Proc Natl Acad Sci U S A. 2009 Nov 17;. [Epub ahead of print]
  PMID: 19920174 [PubMed - as supplied by publisher]
MORE: 1-day-old records for 'Major journals' (2)
MORE: 2-day-old records for 'Major journals' (1)
MORE: 4-day-old records for 'Major journals' (1)
MORE: 8-day-old records for 'Major journals' (1)
MORE: 9-day-old records for 'Major journals' (1)

:::::: Retrieval of selected items
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For your convenience, the following form allows to carry out searches at the US National Library of Medicine (NLM) and PubMed through NCBI:
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:::::: Disclaimer and Copyright

PubCrawler was developed and is hosted by Ken Wolfe's lab in the Genetics Department, Trinity College Dublin, Ireland.
It has no affiliation with NCBI.
This service is free and comes with ABSOLUTELY NO WARRANTY.
It is provided to the public in the hope that it is useful.
All records stem from the National Library of Medicine and were retrieved by PubCrawler through NCBI's E-utils tools.
Please take a look at NCBI's Disclaimer for more information about their disclaimers and copyrights.

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generated by PubCrawler version 2.2 on Friday 20 Nov 2009 at 06:29:04 local time , (access to previous results)
PubCrawler configuration file (pubcrawler.config) reads:

############ PubCrawler configuration file ############
####### (for PubCrawler Version higher than 0.53) ######

############################################################
# #
# lines beginning with hash marks (#) are ignored. #
# #
# PubCrawler home page: #
# http://www.pubcrawler.ie #
# #
# Specify your file locations and search options here. #
# Each line is in the format FIELD space VALUE. #
# Any leading or trailing quotes will be chopped off. #
# Hash marks separate comments from data. #
# You must specify a value for all 6 mandatory fields. #
# #
############################################################

############################################################
################# MANDATORY SETTINGS #######################
############################################################
html_file /Library/WebServer/Documents/local/lab/pubcrawler.html

# html_file is the name of the output HTML file for results
# it will be written to the specified working directory
# unless an absolute pathname is given
viewdays 14
# viewdays is the number of days each document will be shown.

relentrezdate 90
# relentrezdate (relative date of insertion into Entrez)
# is the maximum age (in days) of database entries to be reported.
# NOTE: sometimes records first appear in the databases several
# days or even weeks later than indicated by their database
# date-stamp, i.e. with non-zero values of relentrezdate.
# Therefore relentrezdate needs to be high enough to find these
# records. A relentrezdate of 90 days is suggested (if you make
# relentrezdate too huge the searches will be very slow.)
# other valid entries are:
# '1 year', '2 years', '5 years', '10 years', and 'no limit'

getmax 800 # getmax is the maximum number of documents to be retrieved
# for each search carried out.

fullmax 50 # fullmax is the maximum number of documents for which a full
# report is being presented
# if more documents were retrieved, these can be accessed
# through a hyperlink (in groups of up to fullmax articles)

include_config yes
# include_config (yes/no) specifies whether or not to append
# this config-file to the end of the output file

#-------------------------------------------------------------------#
############################################################
################## OPTIONAL SETTINGS #######################
############################################################

search_URL ''
# URL where searches are being sent to
# defaults to
# http://www.ncbi.nlm.nih.gov/entrez/utils/pmqty.fcgi

neighbour_URL ''
# URL where neighbourhood searches are being sent to
# defaults to
# http://www.ncbi.nlm.nih.gov/entrez/utils/qmap.cgi

retrieve_URL ''
# URL where documents are retrieved from
# defaults to
# http://www.ncbi.nlm.nih.gov/entrez/query.fcgi

work_dir '.'
# specify a directory in which databases, output and log file
# will be located
# if no value given, the current working directory will be used

extra_range 100
# specifies the number of documents combined in a link
# minimum value is 1, defaults to 'fullmax'

check 0
# if set to '1' program will just check all settings
# without performing the actual search
# RECOMMENDED FOR THE FIRST RUN!

prompt 0
# for Mac-users only:
# if this option is set to '1' the program will ask you
# explicitly for command line options
# NOTE: THIS IS NOT SUITABLE FOR AUTOMATED USE!

verbose 0
# verbose 0 runs silently and makes log file
# verbose 1 writes log output on screen

mute 0
# mute 0 writes some messages to STDERR
# mute 1 stops ALL messages going to STDERR
# unless an error was encountered

log_file 'pubCrawler.log'
# name of file for log-output
# (verbose has to be set to '0')

base_URL 'local_file'
# specify a URL, that will be used for
# the 'Back to Top' link in the output page
# 'local_file' makes links relative to results file

#mail joe@hotmail.earth.com
# if the hash mark ('#') at the beginning of the above line
# is removed, PubCrawler will send the results file to
# the given address at the end of each run

#notify jfk@hotmail.earth.com#joe
# if the hash mark ('#') at the beginning of the above line
# is removed, PubCrawler will send a notification to
# the given address (minus '#joe') at the end of each run
# The recipient will be addressed with joe (optional)

lynx ''
# for Unix-users only:
# if you don't want to use the libwww-Perl module and
# have an alternative browser installed, that works from the
# command line, like 'Lynx', you can use it by entering the
# command that evokes it (e.g. lynx '/usr/bin/lynx')
# NOTE: THIS OVERRIDES ANY PROXY SETTINGS!

#header 'head.html'
# specify a location of a header (in HTML-style) that will be used
# for the output file (disabled unless hash mark is removed)

prefix ''
# if you would like a different prefix to be used
# for standard files (configuration, database, log)
# insert it here (default is program name up to first dot):

system ''
# name of operating system
# might need the explicit assignment of an adequate value
# ('MacOS','Win','Unix', or 'Linux')
# if Perl is not configured properly

#### PROXY SETTING (if desired and/or necessary) ####

proxy ''
# insert either a proxy server (eg. 'proxy.domain.com')
# or the address of a proxy configuration file
# if known (eg. 'www.domain.com/proxy.cgi')
# and uncomment

proxy_port ''
# port of the proxy server,defaults to '80'

proxy_auth ''
proxy_pass ''
# in case you need to submit a username and a password
# for accessing your proxy, you can fill it in here:
# CAUTION! Having passwords stored in a file means a
# possible security risk! Please delete after usage
# or use the according command line option!
# !!! Please make sure that the module MIME::Base64 is
# installed for the proxy authorization to work!!!

time_out 180
# specify how many SECONDS to give remote servers
# in creating responses before the library disconnects
# (defaults to 180 seconds if no value is given)

test_URL http://www.ncbi.nlm.nih.gov/
# test-URL for proxy-test

no_test 0
# if a proxy is given, the internet connection is tested
# at the start of the program by default; this can be
# suppressed if a value of '1' is given here

indent 125
# amount of pixels that output is being shifted to the right

no_decap ''
# put 1 inbetween single quotes if you want to disable
# processing of the entrez documents (chopping of head and tail
# and collecting UIs)

spacer ''
# specify a gif that will be inserted in the output to shift
# text past the left, blue column
# (defaults to: http://www.gen.tcd.ie/pubcrawler/pics/spacer.gif)

#-----------------------------------------------------------------------------#
############################################################
################# SEARCH SPECIFICATION #####################
############################################################
###########################################################################
###### Entrez abbreviations for fields #
###### (see http://www4.ncbi.nlm.nih.gov/PubMed/linking.html). #
###### combine fields with AND, OR, BUTNOT and parentheses. #
# #
# for PubMed : one of AFFL, ALL, AUTH, ECNO, JOUR, MESH, MAJR, PAGE, #
# PDAT, PTYP, KYWD, WORD, TITLE, or VOL. #
# for Nucleotide : one of ACCN, AUTH, PDAT, ECNO, FKEY, GENE, JOUR, KYWD, #
# MDAT, ORGN, PROP, PROT, SQID, SLEN, SUBS, or WORD. #
# #
# where ACCN = Accession Number, AFFL = Afilliation, ALL = all fields, #
# AUTH = Author Name, ECNO = E. C. Number, FKEY = Feature Key, #
# GENE = gene name, JOUR =journal name, KYWD = Keywords, #
# MAJR = MeSH major topic, MDAT = modification date, #
# MESH = mesh term,ORGN = organism, PACC = Primary Accesion Number, #
# PAGE = first page, PDAT = publication/creation date, #
# PROP = Properties, PROT = protein name, PTYP = Publication Type, #
# SUBS = Substance, TITL = title word, WORD = text word, #
# VOL = volume. #
###########################################################################

##### Each search-specification has to be written on one line.
##### The first word must specify the database:
##### pubmed, pm_neighbour, genbank, or gb_neighbour
##### Any following words enclosed in single quotes (') will be used
##### as an alias for this query, otherwise they will be considered
##### Entrez-search-terms, as will the rest of the line.

##### You can have as many different searches as you wish. The results of all
##### searches will be combined according to their aliases.

##### You CAN NOT use the same alias for searches at different databases!

##### Write your search descriptions below this line.
##### (Upper/lower case does not matter.)

# The next query searches PubMed for all articles dealing with
# Drosophila's protein kinase genes
#pubmed 'pk genes' Drosophila [ALL] AND ( gene [ALL] or DNA [ALL] ) AND protein kinase [ALL]

# The next five queries search PubMed for articles
# by a few different authors:
#pubmed 'rival labs' Dujon B[AUTH]
#pubmed 'rival labs' Oliver SG[AUTH]
#pubmed 'rival labs' Philippsen P[AUTH]
#pubmed 'rival labs' Smith J[AUTH]
#pubmed 'rival labs' Jones D[AUTH]
#pubmed 'rival labs' Tanaka T[AUTH]
#pubmed 'rival labs' Li W[AUTH]

pubmed 'Picornaviruses' *virus[ALL] AND ( Racaniello V[AUTH] OR Wimmer E[AUTH] OR Lemon S[AUTH] OR Andino R[AUTH] OR Semler B[AUTH] OR Palmenberg A[AUTH] OR Sonenberg N[AUTH] OR Flanegan JB[AUTH] OR Barton DJ[AUTH] OR Nomoto A[AUTH] OR Bergelson J[AUTH] OR CAMERON C[AUTH] OR Kew OM[AUTH] OR Pallansch MA[AUTH] OR Shafren D[AUTH] OR Domingo E[AUTH] OR Kean K[AUTH] OR Agol VI[AUTH] OR Kirkegaard K[AUTH] OR Stanway G[AUTH] OR Ryan MD[AUTH] OR KING AM[AUTH] OR Evans DJ[AUTH] OR Brown TDK[AUTH] OR Minor PD[AUTH] OR Rowlands D[AUTH] OR Belsham G[AUTH] OR Jackson R[AUTH] OR Jackson T[AUTH] OR Knowles N[AUTH] OR Macadam A[AUTH] OR Triantafilou[AUTH] OR Hogle J[AUTH] OR Rossmann MG[AUTH] OR Lea S[AUTH] OR Picornavirus* [TITLE] OR Enterovirus* [TITLE] OR Echovirus* [TITLE] OR Rhinovirus* [TITLE] OR Cardiovirus* [TITLE] OR Aphthovirus* [TITLE] OR Teschovirus* [TITLE] OR Hepatovirus* [TITLE] OR Parechovirus* [TITLE] OR Erbovirus* [TITLE] OR Kobuvirus* [TITLE] )

pubmed 'HCV' *virus[ALL] AND ( Rice C[AUTH] OR Bartenschlager R[AUTH] )

pubmed 'Miscellaneous' *virus[ALL] AND Herbimycin[ALL]

pubmed 'Major journals' ( virus*[TITLE] OR virology[TITLE] ) AND ( Science[Journal Name] OR Nature*[Journal Name] OR 0027-8424[TA] OR Cell[TA] OR EMBO[TA] OR 0028-0836[TA] OR 1087-0156[TA] OR 1465-7392[TA] OR 1061-4036[TA] OR 1529-2908[TA] OR 1078-8956[TA] OR 1548-7091[TA] OR 1740-1526[TA] OR 1545-9993[TA] OR 1072-8368[TA] )

# two searches looking for duplications:
#pubmed 'duplication' ( gene order [All Fields] OR ( polyploid [All Fields] OR "gene number" [All Fields] ) ) AND evolution [All Fields]
#pubmed 'duplication' ( gene [All Fields] OR ( genome [All Fields] OR DNA [All Fields] ) ) AND ( duplicat* [All Fields] OR colinear [All Fields] )

# a long search looking for yeast but not YACs:
#pubmed 'yeast not YAC' ( saccharomyces [All Fields] OR yeast [All Fields] ) AND ( gene [All Fields] OR ( genes [All Fields] OR ( loci [All Fields] OR ( locus [All Fields] OR ( genome [All Fields] OR DNA [All Fields] ) ) ) ) ) BUTNOT ( yeast artificial chromosome [All Fields] OR YAC [All Fields] )

# searching for updates on papers related to
# Watson and Crick's famous one:
#pm_neighbour 'Watson, Crick Paper' 4599080


# The next query searches GenBank for all sequences
# from the organism 'Drosophila melanogaster'
# which contain the word 'kinase' in the annotation text
#genbank 'kinase seq' Drosophila melanogaster [ORGANISM] AND kinase [TEXT]

# searching for updates on sequences related to
# the Candida albicans ssk1p gene:
# disabled because currently not supported by NCBI
#gb_neighbour 'SSK1' 5915906

Page contact: David Evans Last revised: Fri 20 Nov 2009
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