Package: cblaster
cblasterBoth cblaster and clinker can now be used without installation on theCAGECAT webserver.Outlinecblasteris a tool for finding clusters of co-located homologous sequences
in BLAST searches.Given a collection of protein sequences,cblastercan search sequence databases
remotely (via NCBI BLAST API) or locally (viaDIAMOND). Search results are parsed
and filtered based on user thresholds for identity, coverage and e-value. The genomic
coordinates of remaining hits are obtained from the NCBI's Identical Protein
Group (IPG) database (or a local database in local searches). Finally,cblasterscans for instances of collocation and generates visualisations:Installationcblastercan be installed via pip:$pip3installcblaster--useror by cloning the repository and installing:$gitclonehttps://github.com/gamcil/cblaster.git
...
$cdcblaster/
$pip3install.Additionally, we provide executables for Windows and Mac which can be downloadedfrom here.Once installed, make sure you configure cblaster with your email address:$cblasterconfig--emailname@domain.comYou can find example search files, along with generated output, in theexamples folder
of the repository.Dependenciescblasteris tested on Python 3.6, and its only external Python dependency is
therequestsmodule (used for interaction with NCBI APIs).
If you want to perform local searches, you should havediamondinstalled and available
on your system $PATH.cblasterwill throw an error if a local search is started but it cannot finddiamondordiamond-aligner(alias when installed via apt) on the system.Usagecblasteraccepts FASTA files and collections of valid NCBI sequence identifiers
(GIs, accession numbers) as input.
A remote search can be performed as simply as:$cblastersearch--query_filequery.fastaFor example, to remotely search theburnettramic acids gene cluster,bua, against the NCBI's nr database:$cblastersearch-qfbua.fasta[12:14:17]INFO-Startingcblasterinremotemode[12:14:17]INFO-Launchingnewsearch[12:14:19]INFO-RequestIdentifier(RID):WHS0UGYJ015[12:14:19]INFO-RequestTimeOfExecution(RTOE):25s[12:14:44]INFO-PollingNCBIforcompletionstatus[12:14:44]INFO-Checkingsearchstatus...[12:15:44]INFO-Checkingsearchstatus...[12:16:44]INFO-Checkingsearchstatus...[12:16:46]INFO-Searchhascompletedsuccessfully![12:16:46]INFO-RetrievingresultsforsearchWHS0UGYJ015[12:16:51]INFO-Parsingresults...[12:16:51]INFO-Found3944hitsmeetingscorethresholds[12:16:51]INFO-Fetchinggenomiccontextofhits[12:17:14]INFO-Searchingforclusteredhitsacross705organisms[12:17:14]INFO-Writingsummaryto<stdout>

AspergillusmulundensisDSM5745================================NW_020797889.1
--------------
QuerySubjectIdentityCoverageE-valueBitscoreStartEndStrand
QBE85641.1XP_026607259.175.5699.5918074217178811719409-
QBE85642.1XP_026607260.189.916100066717196501720797+
QBE85643.1XP_026607261.189.53283.1169083217214941722934+
QBE85644.1XP_026607262.164.82998.92186.51e-15745517232521724467-
QBE85645.1XP_026607263.169.971006.93e-15744917251131726277-
QBE85646.1XP_026607264.182.75996.8447067017268921728302+
QBE85647.1XP_026607265.172.67499.2048076417297351731338+
QBE85648.1XP_026607266.156.09898.3244.24e-6420517317011732402-
QBE85649.1XP_026607267.179.62399.87460657317328201745289+

...A query sequence absence/presence matrix can be generated using the--binaryargument:Organism                                   Scaffold        Start    End      QBE85641.1  QBE85642.1  QBE85643.1  QBE85644.1  QBE85645.1  QBE85646.1  QBE85647.1  QBE85648.1  QBE85649.1
Aspergillus mulundensis DSM 5745           NW_020797889.1  1717881  1745289  1           1           1           1           1           1           1           1           1         
Aspergillus versicolor CBS 583.65          KV878126.1      3162095  3187090  1           1           1           0           1           1           1           1           1         
Pseudomassariella vexata CBS 129021        MCFJ01000004.1  1606356  1628483  1           1           1           0           0           1           0           1           1         
Hypoxylon sp. CO27-5                       KZ112517.1      92119    112957   1           1           1           0           0           0           1           0           1         
Hypoxylon sp. EC38                         KZ111255.1      514739   535366   1           1           1           0           0           0           1           0           1         
Epicoccum nigrum ICMP 19927                KZ107839.1      2116719  2142558  1           1           0           0           0           1           1           0           1         
Aureobasidium subglaciale EXF-2481         NW_013566983.1  700476   718693   1           1           0           0           0           1           1           0           0         
Aureobasidium pullulans EXF-6514           QZBF01000009.1  18721    34295    1           1           0           0           0           1           1           0           0         
Aureobasidium pullulans EXF-5628           QZBI01000512.1  329      13401    1           0           0           0           0           1           1           0           0cblastercan also generate fully interactive visualisations of the binary
table. To view an example, clickhere.For further usage examples and API documentation, please refer to thedocumentation.CitationIf you found this tool useful, please cite:Cameron L M Gilchrist, Thomas J Booth, Bram van Wersch, Liana van Grieken, Marnix H Medema, Yit-Heng Chooi, cblaster: a remote search tool for rapid identification and visualisation of homologous gene clusters, Bioinformatics Advances, 2021;, vbab016, https://doi.org/10.1093/bioadv/vbab016cblastermakes use of the following tools:Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60 (2015).

Acland, A. et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 42, 7–17 (2014).