{"id":26573235,"url":"https://github.com/linsalrob/phisigns","last_synced_at":"2025-03-23T00:39:53.399Z","repository":{"id":89477507,"uuid":"104136260","full_name":"linsalrob/PhiSigns","owner":"linsalrob","description":"PhiSiGns is a web-based and standalone application that provides a simple and convenient tool to identify signature genes and design primers for PCR amplification of related genes from environmental samples","archived":false,"fork":false,"pushed_at":"2024-09-07T02:48:36.000Z","size":23,"stargazers_count":1,"open_issues_count":0,"forks_count":1,"subscribers_count":4,"default_branch":"master","last_synced_at":"2024-09-07T04:49:26.196Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Perl","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/linsalrob.png","metadata":{"files":{"readme":"README.txt","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2017-09-19T22:34:52.000Z","updated_at":"2017-09-21T11:29:14.000Z","dependencies_parsed_at":null,"dependency_job_id":"3b032d09-cb55-4631-a555-27a457447464","html_url":"https://github.com/linsalrob/PhiSigns","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linsalrob%2FPhiSigns","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linsalrob%2FPhiSigns/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linsalrob%2FPhiSigns/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linsalrob%2FPhiSigns/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/linsalrob","download_url":"https://codeload.github.com/linsalrob/PhiSigns/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245040190,"owners_count":20551299,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2025-03-23T00:39:52.791Z","updated_at":"2025-03-23T00:39:53.336Z","avatar_url":"https://github.com/linsalrob.png","language":"Perl","funding_links":[],"categories":[],"sub_categories":[],"readme":"PhiSiGns\n~~~~~~~~\n\n\nDESCRIPTION\n-----------\nA computational tool for the identification of phage signature genes and PCR primer design\n\n\nPURPOSE\n-------\nPhiSiGns is intended for the phage biologists who are interested  \n\n1) in finding shared conserved genes in phages for evolution-based studies and/or\n\n2) in designing primers on shared genes that can be used to discover unknown phages in the environment \n\n\n\nSTANDALONE Vs. WEB-BASED VERSION\n--------------------------------\nPhiSiGns is a standalone and web-based application. Both versions provide the same features and results, but differ in the following:\n\n1) The standalone version does not come with a phage genome database or precalculated BLASTP outputs. The user inputs the phage genomes to be compared for signature gene identification and primer design in an input txt file. The phage genomes are input as NCBI refseq numbers (see Standalone version - running mode). The GenBank files for the user-selected set of phage genomes are then obtained from NCBI and the gene annotations for the protein coding regions are imported accordingly. In contrast, the PhiSiGns web-based version consists of a database of 636 phages and 33 archaeal viruses (derived from the phage database on the PhAnToMe website, Feb 2011 [http://www.phantome.org/Downloads]), and pre-calculated BLASTP outputs for all these genomes (computed using PhiSiGns at an E-value cut-off of 10). The gene annotations are imported from the SEED [http://www.theseed.org/wiki/Home_of_the_SEED] and the proteins that lack annotation are extracted from GenBank. Therefore, with the standalone version users have the ability to compare phage genomes that are not part of the web-based PhiSiGns phage database.\n\n2) The standalone version does not provide the option to select/deselect genes within the selected signature gene group for alignment and primer design. However, users can upload their own alignment containing only the sequences of interest.\n\n\nSTANDALONE VERSION - PREREQUISITES\n----------------------------------\nStandalone version is a perl script (phisigns.pl) and requires the following softwares and modules to run:\n\nResources\n\tDirect internet connection\n\nSoftware\n\tBLASTALL (Blast standalone package)\n\tCLUSTALW 1.8 (Multiple sequence alignment tool)\n\t\nBioPerl modules \n\tBio::Seq\n\tBio::SeqIO\n\tBio::SeqFeature::Generic\n\tBio::DB::GenBank\n\tBio::DB::Fasta\n\tBio::Index::Fasta\n\tBio::Tools::Run::StandAloneBlast\n\tBio::Tools::Run::Alignment::Clustalw\n\tBio::Align::Utilities qw(aa_to_dna_aln)\n\tBio::AlignIO;\n\nPerl modules\n\tGetopt::Long\n\tFile::Basename\n\tList::Util qw(max)\n\nFiles\n\tinput.txt\n\nAlso, you must have administrative rights to create, delete, read, or write files in the PhiSiGns working directory whereever located on your computer.\n \n\nSTANDALONE VERSION - SETTING VARIABLES\n--------------------------------------\nFollowing variables must be set before running phisigns.pl:\n\n$BLASTALL (BLASTALL executable directory path)\nExample: $BLASTALL  = '/home/user/blast/bin/blastall'\n\n$FORMATDB (FORMATDB executable directory path)\nExample: $FORMATDB = '/home/user/blast/bin/formatdb'\n\n$ENV{CLUSTALDIR} (CLUSTALW directory path)\nExample: $ENV{CLUSTALDIR} = '/home/user/clustalw1.8/' \n\n\nSTANDALONE VERSION - COMMAND OPTIONS\n------------------------------------\n\nOption\t  Description\t\t\t   Default Argument\n___________________________________________________________\n-d\t  PhiSiGns working directory path     -\t   string\n-m\t  run mode\t\t\t      0\t      int\n-e\t  BLAST E-value cut-off\t\t     10\t    float\n-c\t  BLAST coverage cut-off\t     10\t    float\n-i\t  input file\t\t\t      -\t   string\n-g\t  selected SiG_# for primer design    -\t   string\n-a\t  user uploaded alignment file\t      -\t   string\n-aln_only Display default CLUSTALW alignment  -\t     none\n-id\t  id of current job\t\t      -\t   string\n\n\nSTANDALONE VERSION - RUNNING MODE\n---------------------------------\nThere are two modes to run PhiSiGns (phisigns.pl):\n\n\nMODE 0\n------\n\nIdentifies the signature genes amongst the user-selected phage genomes as listed in the input file ('-i') saved under the PhiSiGns working directory. The input file must include the NCBI refseq number for the phage genomes to be compared for signature gene identification and primer design. Type the following command line to execute phisigns.pl in Mode = 0:\n\nExample:  % phisigns.pl -d /home/user/phisigns/ -m 0 -e 0.1 -c 25 -i input.txt -id test\n\nBLAST E-value cut-off ('-e') and coverage ('-c') cut-off can be set by the user, if not specified a default value of 10 and 10 is used, respectively. Once the above command is executed and finished running, data and result files are generated with respect to the job id specified ('-id') in the command line under the PhiSiGns working directory.\n\nOutput files:\n\tdata/.blastoutput\t\t\tBLASTALL results for the selected phage genomes\n\tdata/.cdstbl.ffd\t\t\tPhage CDS table\n\tdata/.cds_nucleotide.fa\t\t\tCDS Nucleotide sequences\n\toutput/.sig_gps.txt\t\t\tshort list of identified signature genes (SiG's)\n\toutput/.sig_gps_detail.txt\t\tdetailed list of SiG's\n\toutput/.log.txt\t\t\t\tphisigns log file\n\n\nMODE 1\n------\n\nDesign PCR primer pairs for a selected signature gene (SiG_#) from the list of identified SiG's ('.sig_gps.txt' or .sig_gps_detail.txt' file) generated in Mode = 0. The primers are designed taking into account the minimum and maximum values specified for the primer parameters as in the pparams.txt file. Users can modify the values of these parameters to their preference. \n\nPrimer Parameters options\n\nFlag\t Description\t\t\t\tDefault\t\t    Range\n_________________________________________________________________________\nminl\t min primer length\t\t\t  16\t\t    10-28\nmaxl\t max primer length\t\t\t  28\t\t    10-28\nmingc\t min GC content\t\t\t\t  30\t\t    20-80\nmaxgc\t max GC content\t\t\t\t  80\t\t    30-80\nminbtm\t min Basic Melting Temperature\t\t  30\t\t    30-80\nmaxbtm\t max Basic Melting Temperature\t\t  80\t\t    30-80\nminstm\t min Salt Adjusted Temperature\t\t  30\t\t    30-80\nmaxstm\t max Salt Adjusted Temperature\t\t  80\t\t    30-80\nminnnh\t min Nearest Neighbor Temperature\t  30\t\t    30-80\nmaxnnh\t max Nearest Neighbor Temperature\t  80\t\t    30-80\nmindg\t min delta G for a primer\t\t -20\t\t   -30-0\nminpl\t min product length\t\t\t 400\t\t 100-2500\nmaxpl\t max product length\t\t\t2000\t\t 100-2500\ndgn\t primer degeneracy \t\t\t1000\t\t   1-1000\ngcclamp\t 3' GC clamp\t\t\t           y\t\t   y or n\nmax3stb  maximum 3' stability\t\t\t   y\t\t   y or n\ncompl\t Complementarity\t\t\t   y\t\t   y or n\n\n\nType the following command line to execute phisigns.pl in Mode = 1 to only display program generated alignment for a selected signature gene:\n\nExample:  % phisigns.pl -d /home/user/phisigns/ -m 1 -g SiG_5 -aln_only -id test\n\n\nType the following command line to execute phisigns.pl in Mode = 1 with the program generated alignment:\n\nExample:  % phisigns.pl -d /home/user/phisigns/ -m 1 -g SiG_5 -id test\n\n\nUsers can also upload their own nucleotide sequence alignment (in CLUSTALW format only with '.aln' file extension) for the selected signature gene group to design PCR primer pairs.  The user uploaded alignment file should be under the phisigns working directory. \n\nType the following command line to execute phisigns.pl in Mode = 1 with a user-generated alignment:\n\nExample:  % phisigns.pl -d /home/user/phisigns/ -m 1 -a test.aln -id test\n\nOnce the above command is executed and finished running, results files for the user uploaded alignment are generated with respect to the job id specified ('-id') in the command line under the phisigns working directory.\n\nOutput files:\n\toutput/.seqs\t\t\tsequences in FASTA format for the user-selected SiG_#\n\toutput/.aln\t\t\tnucleotide sequence CLUSTALW alignment for the selected SiG_#\n\toutput/.pairs.txt\t\tshort list of potential primer pairs found for the selected SiG_#\n\toutput/.pairs_detail.txt\tdetailed list of the potential primer pairs found for the selected SiG_#\n\toutput/.log.txt\t\t\tphisigns log file\n\n\nNote: PhiSiGns (phisigns.pl) in Mode = 1 will execute only after PhiSiGns is executed in Mode = 0. Unless the selected set of phage genomes is different, Mode = 0 need not be executed more than once. To design PCR primer pairs with a user-uploaded alignment Mode = 1 can be executed without running Mode = 0 first. \n\n\nWEB VERSION -  RUNNING\n----------------------\nA. Identify signature genes\n\t1. Select and add phage genomes of interest from the list of available phage genomes\n\t2. Select BLAST E-value and coverage cut-off for similarity searches\n\t3. Click on \"Get Signature Genes\"\n\t4. View the list on the webpage or download the table on a local machine\nB. Design PCR primer pairs\n\t1. Select a signature gene from the list of identified signature genes amongst the phage genomes of interest\n\t2. Select minimum and maximum primer parameter values [optional]\n\t3. Select/deselect genes within the selected signature gene group for alignment and primer design [optional]\n\t4. View program generated CLUSTALW alignment for selected genes [optional]\n\t5. Upload your own nucleotide sequence alignment for the selected signature gene [optional]\n\t6. Click on \"Design Primers for Selected SiG Genes\"\n\t7. View the results on the webpage or download them on a local machine\n\nFor more details on web version, please see http://phisigns.sourceforge.net/\n\n\nWEB VERSION - DEPENDENCIES\n--------------------------\nThe perl script require these Perl modules:\n\tCGI qw(:standard :html3)\n\tCGI::Carp qw(fatalsToBrowser)\n\tFcntl qw(:DEFAULT :flock)\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flinsalrob%2Fphisigns","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flinsalrob%2Fphisigns","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flinsalrob%2Fphisigns/lists"}