Virus:Article Title: DeepMineLys: Deep mining of phage lysins from human microbiome.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains E. coli DH5a Tsingke Biotech Cat# TSC-C01 E. coli BL21(DE3) TransGen Biotech Cat# CD601-02 Pseudomonas aeruginosa Prof. Fuquan Hu (Third Military Medical University, China) PAO1 Pseudomonas aeruginosa Guangdong Microbial Culture Center, China (GDMCC) ATCC 9027, ATCC 15442, ATCC 10145 and ATCC 27853 Staphylococcus aureus Guangdong Microbial Culture Center, China (GDMCC) ATCC 6538 Listeria monocytogenes China Center of Industrial Culture Collection (CICC) CICC 21634 Chemicals, peptides, and recombinant proteins KWK peptide Chen et al.55 N/A Deposited data GPD database and metadata Camarillo-Guerrero et al.12 http://ftp.ebi.ac.uk/pub/databases/ metagenomics/genome_sets/gut_phage_database GutV metagenomics assembly data This study NCBI SRA Bioproject: PRJNA1135322; https://www.ncbi.nlm.nih.gov/sra Skin metagenomics data the National Gene Bank (CNGB) Sequence Archiving CNGB Project ID: CNP0000635; https://db.cngb.org/ Oligonucleotides See Table S5 This study N/A Software and algorithms Tasks assessing protein embeddings (TAPE) Rao et al.25 https://github.com/songlab-cal/tape MCL v14-137 Li et al.32 https://www.micans.org/mcl CD-HIT v4.8.1 Li and Godzik,49 https://github.com/weizhongli/cdhit/wiki iPHoP Roux et al.50 https://bitbucket.org/srouxjgi/iphop InterProScan Quevillon et al.51 http://www.ebi.ac.uk/InterProScan Seqkit toolkit v2.2.0 Shen et al.62 https://bioinf.shenwei.me/seqkit FastQC v0.11.7 The Staff of Babraham Bioinformatics http://www.bioinformatics.babraham. ac.uk/projects/fastqc Trimmomatic v0.36 Bolger et al.63 https://github.com/usadellab/Trimmomatic BWA v0.7.17-r1188 Li and Durbin,64 https://github.com/lh3/bwa MEGAHIT v1.1.3 Li et al.65 https://github.com/voutcn/megahit MetaQUAST v4.6.3 Mikheenko et al.66 https://bioinf.spbau.ru/metaquast VAMB v3.0.7 Nissen et al.67 https://github.com/RasmussenLab/vamb PHAMB Johansen et al.68 https://github.com/RasmussenLab/phamb VirFinder v1.1 Ren et al.69 https://github.com/jessieren/VirFinder CheckV v0.9.0 Nayfach et al.70 https://bitbucket.org/berkeleylab/checkv/src/master Prodigal v2.6.3 Hyatt et al.71 https://github.com/hyattpd/Prodigal BLASTp v2.9.0+ Altschul et al.72 https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/ Vennerable (R package) N/A https://github.com/js229/Vennerable Peptides (R package) Osorio et al.73 https://github.com/dosorio/Peptides (Continued on next page) Cell Reports 43, 114583, August 27, 2024 13 ..
Recombinant:Article Title: DeepMineLys: Deep mining of phage lysins from human microbiome.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains E. coli DH5a Tsingke Biotech Cat# TSC-C01 E. coli BL21(DE3) TransGen Biotech Cat# CD601-02 Pseudomonas aeruginosa Prof. Fuquan Hu (Third Military Medical University, China) PAO1 Pseudomonas aeruginosa Guangdong Microbial Culture Center, China (GDMCC) ATCC 9027, ATCC 15442, ATCC 10145 and ATCC 27853 Staphylococcus aureus Guangdong Microbial Culture Center, China (GDMCC) ATCC 6538 Listeria monocytogenes China Center of Industrial Culture Collection (CICC) CICC 21634 Chemicals, peptides, and recombinant proteins KWK peptide Chen et al.55 N/A Deposited data GPD database and metadata Camarillo-Guerrero et al.12 http://ftp.ebi.ac.uk/pub/databases/ metagenomics/genome_sets/gut_phage_database GutV metagenomics assembly data This study NCBI SRA Bioproject: PRJNA1135322; https://www.ncbi.nlm.nih.gov/sra Skin metagenomics data the National Gene Bank (CNGB) Sequence Archiving CNGB Project ID: CNP0000635; https://db.cngb.org/ Oligonucleotides See Table S5 This study N/A Software and algorithms Tasks assessing protein embeddings (TAPE) Rao et al.25 https://github.com/songlab-cal/tape MCL v14-137 Li et al.32 https://www.micans.org/mcl CD-HIT v4.8.1 Li and Godzik,49 https://github.com/weizhongli/cdhit/wiki iPHoP Roux et al.50 https://bitbucket.org/srouxjgi/iphop InterProScan Quevillon et al.51 http://www.ebi.ac.uk/InterProScan Seqkit toolkit v2.2.0 Shen et al.62 https://bioinf.shenwei.me/seqkit FastQC v0.11.7 The Staff of Babraham Bioinformatics http://www.bioinformatics.babraham. ac.uk/projects/fastqc Trimmomatic v0.36 Bolger et al.63 https://github.com/usadellab/Trimmomatic BWA v0.7.17-r1188 Li and Durbin,64 https://github.com/lh3/bwa MEGAHIT v1.1.3 Li et al.65 https://github.com/voutcn/megahit MetaQUAST v4.6.3 Mikheenko et al.66 https://bioinf.spbau.ru/metaquast VAMB v3.0.7 Nissen et al.67 https://github.com/RasmussenLab/vamb PHAMB Johansen et al.68 https://github.com/RasmussenLab/phamb VirFinder v1.1 Ren et al.69 https://github.com/jessieren/VirFinder CheckV v0.9.0 Nayfach et al.70 https://bitbucket.org/berkeleylab/checkv/src/master Prodigal v2.6.3 Hyatt et al.71 https://github.com/hyattpd/Prodigal BLASTp v2.9.0+ Altschul et al.72 https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/ Vennerable (R package) N/A https://github.com/js229/Vennerable Peptides (R package) Osorio et al.73 https://github.com/dosorio/Peptides (Continued on next page) Cell Reports 43, 114583, August 27, 2024 13 ..
Metagenomics:Article Title: DeepMineLys: Deep mining of phage lysins from human microbiome.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains E. coli DH5a Tsingke Biotech Cat# TSC-C01 E. coli BL21(DE3) TransGen Biotech Cat# CD601-02 Pseudomonas aeruginosa Prof. Fuquan Hu (Third Military Medical University, China) PAO1 Pseudomonas aeruginosa Guangdong Microbial Culture Center, China (GDMCC) ATCC 9027, ATCC 15442, ATCC 10145 and ATCC 27853 Staphylococcus aureus Guangdong Microbial Culture Center, China (GDMCC) ATCC 6538 Listeria monocytogenes China Center of Industrial Culture Collection (CICC) CICC 21634 Chemicals, peptides, and recombinant proteins KWK peptide Chen et al.55 N/A Deposited data GPD database and metadata Camarillo-Guerrero et al.12 http://ftp.ebi.ac.uk/pub/databases/ metagenomics/genome_sets/gut_phage_database GutV metagenomics assembly data This study NCBI SRA Bioproject: PRJNA1135322; https://www.ncbi.nlm.nih.gov/sra Skin metagenomics data the National Gene Bank (CNGB) Sequence Archiving CNGB Project ID: CNP0000635; https://db.cngb.org/ Oligonucleotides See Table S5 This study N/A Software and algorithms Tasks assessing protein embeddings (TAPE) Rao et al.25 https://github.com/songlab-cal/tape MCL v14-137 Li et al.32 https://www.micans.org/mcl CD-HIT v4.8.1 Li and Godzik,49 https://github.com/weizhongli/cdhit/wiki iPHoP Roux et al.50 https://bitbucket.org/srouxjgi/iphop InterProScan Quevillon et al.51 http://www.ebi.ac.uk/InterProScan Seqkit toolkit v2.2.0 Shen et al.62 https://bioinf.shenwei.me/seqkit FastQC v0.11.7 The Staff of Babraham Bioinformatics http://www.bioinformatics.babraham. ac.uk/projects/fastqc Trimmomatic v0.36 Bolger et al.63 https://github.com/usadellab/Trimmomatic BWA v0.7.17-r1188 Li and Durbin,64 https://github.com/lh3/bwa MEGAHIT v1.1.3 Li et al.65 https://github.com/voutcn/megahit MetaQUAST v4.6.3 Mikheenko et al.66 https://bioinf.spbau.ru/metaquast VAMB v3.0.7 Nissen et al.67 https://github.com/RasmussenLab/vamb PHAMB Johansen et al.68 https://github.com/RasmussenLab/phamb VirFinder v1.1 Ren et al.69 https://github.com/jessieren/VirFinder CheckV v0.9.0 Nayfach et al.70 https://bitbucket.org/berkeleylab/checkv/src/master Prodigal v2.6.3 Hyatt et al.71 https://github.com/hyattpd/Prodigal BLASTp v2.9.0+ Altschul et al.72 https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/ Vennerable (R package) N/A https://github.com/js229/Vennerable Peptides (R package) Osorio et al.73 https://github.com/dosorio/Peptides (Continued on next page) Cell Reports 43, 114583, August 27, 2024 13 ..
Sequencing:Article Title: DeepMineLys: Deep mining of phage lysins from human microbiome.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains E. coli DH5a Tsingke Biotech Cat# TSC-C01 E. coli BL21(DE3) TransGen Biotech Cat# CD601-02 Pseudomonas aeruginosa Prof. Fuquan Hu (Third Military Medical University, China) PAO1 Pseudomonas aeruginosa Guangdong Microbial Culture Center, China (GDMCC) ATCC 9027, ATCC 15442, ATCC 10145 and ATCC 27853 Staphylococcus aureus Guangdong Microbial Culture Center, China (GDMCC) ATCC 6538 Listeria monocytogenes China Center of Industrial Culture Collection (CICC) CICC 21634 Chemicals, peptides, and recombinant proteins KWK peptide Chen et al.55 N/A Deposited data GPD database and metadata Camarillo-Guerrero et al.12 http://ftp.ebi.ac.uk/pub/databases/ metagenomics/genome_sets/gut_phage_database GutV metagenomics assembly data This study NCBI SRA Bioproject: PRJNA1135322; https://www.ncbi.nlm.nih.gov/sra Skin metagenomics data the National Gene Bank (CNGB) Sequence Archiving CNGB Project ID: CNP0000635; https://db.cngb.org/ Oligonucleotides See Table S5 This study N/A Software and algorithms Tasks assessing protein embeddings (TAPE) Rao et al.25 https://github.com/songlab-cal/tape MCL v14-137 Li et al.32 https://www.micans.org/mcl CD-HIT v4.8.1 Li and Godzik,49 https://github.com/weizhongli/cdhit/wiki iPHoP Roux et al.50 https://bitbucket.org/srouxjgi/iphop InterProScan Quevillon et al.51 http://www.ebi.ac.uk/InterProScan Seqkit toolkit v2.2.0 Shen et al.62 https://bioinf.shenwei.me/seqkit FastQC v0.11.7 The Staff of Babraham Bioinformatics http://www.bioinformatics.babraham. ac.uk/projects/fastqc Trimmomatic v0.36 Bolger et al.63 https://github.com/usadellab/Trimmomatic BWA v0.7.17-r1188 Li and Durbin,64 https://github.com/lh3/bwa MEGAHIT v1.1.3 Li et al.65 https://github.com/voutcn/megahit MetaQUAST v4.6.3 Mikheenko et al.66 https://bioinf.spbau.ru/metaquast VAMB v3.0.7 Nissen et al.67 https://github.com/RasmussenLab/vamb PHAMB Johansen et al.68 https://github.com/RasmussenLab/phamb VirFinder v1.1 Ren et al.69 https://github.com/jessieren/VirFinder CheckV v0.9.0 Nayfach et al.70 https://bitbucket.org/berkeleylab/checkv/src/master Prodigal v2.6.3 Hyatt et al.71 https://github.com/hyattpd/Prodigal BLASTp v2.9.0+ Altschul et al.72 https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/ Vennerable (R package) N/A https://github.com/js229/Vennerable Peptides (R package) Osorio et al.73 https://github.com/dosorio/Peptides (Continued on next page) Cell Reports 43, 114583, August 27, 2024 13 ..
Software:Article Title: DeepMineLys: Deep mining of phage lysins from human microbiome.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains E. coli DH5a Tsingke Biotech Cat# TSC-C01 E. coli BL21(DE3) TransGen Biotech Cat# CD601-02 Pseudomonas aeruginosa Prof. Fuquan Hu (Third Military Medical University, China) PAO1 Pseudomonas aeruginosa Guangdong Microbial Culture Center, China (GDMCC) ATCC 9027, ATCC 15442, ATCC 10145 and ATCC 27853 Staphylococcus aureus Guangdong Microbial Culture Center, China (GDMCC) ATCC 6538 Listeria monocytogenes China Center of Industrial Culture Collection (CICC) CICC 21634 Chemicals, peptides, and recombinant proteins KWK peptide Chen et al.55 N/A Deposited data GPD database and metadata Camarillo-Guerrero et al.12 http://ftp.ebi.ac.uk/pub/databases/ metagenomics/genome_sets/gut_phage_database GutV metagenomics assembly data This study NCBI SRA Bioproject: PRJNA1135322; https://www.ncbi.nlm.nih.gov/sra Skin metagenomics data the National Gene Bank (CNGB) Sequence Archiving CNGB Project ID: CNP0000635; https://db.cngb.org/ Oligonucleotides See Table S5 This study N/A Software and algorithms Tasks assessing protein embeddings (TAPE) Rao et al.25 https://github.com/songlab-cal/tape MCL v14-137 Li et al.32 https://www.micans.org/mcl CD-HIT v4.8.1 Li and Godzik,49 https://github.com/weizhongli/cdhit/wiki iPHoP Roux et al.50 https://bitbucket.org/srouxjgi/iphop InterProScan Quevillon et al.51 http://www.ebi.ac.uk/InterProScan Seqkit toolkit v2.2.0 Shen et al.62 https://bioinf.shenwei.me/seqkit FastQC v0.11.7 The Staff of Babraham Bioinformatics http://www.bioinformatics.babraham. ac.uk/projects/fastqc Trimmomatic v0.36 Bolger et al.63 https://github.com/usadellab/Trimmomatic BWA v0.7.17-r1188 Li and Durbin,64 https://github.com/lh3/bwa MEGAHIT v1.1.3 Li et al.65 https://github.com/voutcn/megahit MetaQUAST v4.6.3 Mikheenko et al.66 https://bioinf.spbau.ru/metaquast VAMB v3.0.7 Nissen et al.67 https://github.com/RasmussenLab/vamb PHAMB Johansen et al.68 https://github.com/RasmussenLab/phamb VirFinder v1.1 Ren et al.69 https://github.com/jessieren/VirFinder CheckV v0.9.0 Nayfach et al.70 https://bitbucket.org/berkeleylab/checkv/src/master Prodigal v2.6.3 Hyatt et al.71 https://github.com/hyattpd/Prodigal BLASTp v2.9.0+ Altschul et al.72 https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/ Vennerable (R package) N/A https://github.com/js229/Vennerable Peptides (R package) Osorio et al.73 https://github.com/dosorio/Peptides (Continued on next page) Cell Reports 43, 114583, August 27, 2024 13 ..
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