[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"doc-detail-183999-en":3,"doc-seo-183999-105":30,"detail-sidebar-cat-0-en-105":91},{"code":4,"msg":5,"data":6},0,"success",{"doc_id":7,"user_id":8,"nickname":9,"user_avatar":10,"doc_module":4,"category_id":11,"category_name":12,"doc_title":13,"doc_description":14,"doc_content":15,"file_id":16,"file_url":17,"file_type":18,"file_size":19,"view_count":4,"is_deleted":4,"is_public":20,"is_downloadable":20,"audit_status":20,"page_count":21,"language":22,"language_code":23,"site_id":24,"html_lang":23,"table_of_contents":25,"faqs":26,"seo_title":27,"seo_description":14,"update_tm":28,"read_time":29},183999,549768702563,"Fahsai","https://ap-avatar.wpscdn.com/avatar/8000c4aa63b76e948b?x-image-process=image/resize,m_fixed,w_180,h_180&k=1786536092046926083",8,"Research & Report","Protein Homology Search Performance Comparison - BLAST and PSI-BLAST Results Tables","Protein homology search performance is evaluated through comparative tables of BLAST variants and PSI-BLAST across multiple protein families. The document analyzes computational overhead, assesses whether detected hits qualify for ungapped extension, and contrasts ungapped versus gapped extension outcomes. It reports SWISS-PROT accessions, E-value statistics, and counts of sequences passing thresholds, then further summarizes alignment scores using Smith–Waterman and scores returned by Original BLAST, Gapped BLAST, and PSI-BLAST, including normalized running time.","|  | Overhead: database scanning, output, etc. | Calculating whether hits\u003Cbr>qualify for ungapped extension | Ungapped extensions | Gapped extensions |\n| --- | --- | --- | --- | --- |\n| Original BLAST | 8 (8%) |  | 92 (92%) |  |\n| Gapped BLAST | 8 (24%) | 12 (37%) | 5 (15%) | 8 (24%) |\n\n| Protein family | SWISS-PROT\u003Cbr>accession no. of query | Original BLAST |  |  | Gapped BLAST |  |  | PSI-BLAST |  |  |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n|  |  |  |  |  |  |  |  | Low E-value | No. of seqs with E-value ≤1 ≤10 |  |\n|  |  | Low E-value | No. of seqs with E-value ≤1 ≤10 |  | Low E-value | No. of seqs with E-value ≤1 ≤10 |  |  |  |  |\n| Serine protease | P00762 | 0.86 | 1 | 7 | 3.0 | 0 | 4 | 0.94 | 1 | 8 |\n| Serine protease inhibitor | P01008 | 3.9 | 0 | 4 | 0.078 | 1 | 9 | 1.5 | 0 | 9 |\n| Ras | P01111 | 3.4 | 0 | 8 | 3.4 | 0 | 7 | 1.1 | 0 | 9 |\n| Globin | P02232 | 2.4 | 0 | 7 | 2.8 | 0 | 5 | 8.2 | 0 | 2 |\n| Hemagglutinin | P03435 | 0.11 | 2 | 11 | 0.46 | 3 | 16 | 0.87 | 1 | 8 |\n| Interferon α | P05013 | 2.4 | 0 | 6 | 0.27 | 2 | 4 | 0.11 | 2 | 11 |\n| Alcohol dehydrogenase | P07327 | 1.5 | 0 | 2 | 0.80 | 1 | 5 | 1.5 | 0 | 9 |\n| Histocompatibility antigen | P10318 | 0.91 | 1 | 7 | 0.13 | 1 | 7 | 0.0031 | 2 | 6 |\n| Cytochrome P450 | P10635 | 0.84 | 2 | 5 | 8.5 | 0 | 3 | 0.46 | 1 | 15 |\n| Glutathione transferase | P14942 | 1.0 | 1 | 10 | 3.3 | 0 | 3 | 0.30 | 2 | 9 |\n| H+-transporting ATP synthase | P20705 | 0.012 | 1 | 8 | 0.26 | 2 | 14 | 0.79 | 2 | 10 |\n| Average (median or mean) |  | 1.0 | 0.7 | 6.8 | 0.80 | 0.9 | 7.0 | 0.87 | 1.0 | 8.7 |\n\n\n| Protein family | Query | Smith–Waterman | Original BLAST | Gapped BLAST | PSI-BLAST |\n| --- | --- | --- | --- | --- | --- |\n| Serine protease | P00762 | 275 | 273 | 275 | 286 |\n| Serine protease inhibitor | P01008 | 108 | 105 | 108 | 111 |\n| Ras | P01111 | 255 | 249 | 252 | 375 |\n| Globin | P02232 | 28 | 26 | 28 | 623 |\n| Hemagglutinin | P03435 | 128 | 114 | 128 | 130 |\n| Interferon α | P05013 | 53 | 53 | 53 | 53 |\n| Alcohol dehydrogenase | P07327 | 138 | 128 | 137 | 160 |\n| Histocompatibility antigen | P10318 | 262 | 241 | 261 | 338 |\n| Cytochrome P450 | P10635 | 211 | 197 | 211 | 224 |\n| Glutathione transferase | P14942 | 83 | 79 | 81 | 142 |\n| H+-transporting ATP synthase | P20705 | 198 | 191 | 197 | 207 |\n| Normalized running time |  | 36 | 1.0 | 0.34 | 0.87 |","cbCaiqfX0dLJTd9i","https://ap.wps.com/l/cbCaiqfX0dLJTd9i","pdf",210077,1,14,"English","en",105,"# Performance evaluation\n## Overhead and extension criteria\n## Comparative results by protein family\n## Alignment scores and running time","[{\"question\":\"What search methods are compared in the document?\",\"answer\":\"The document compares Original BLAST, Gapped BLAST, and PSI-BLAST, alongside Smith–Waterman alignment scores in a summary table.\"},{\"question\":\"How are ungapped and gapped extensions evaluated?\",\"answer\":\"It reports whether hits qualify for ungapped extension and provides separate outcomes for ungapped extensions versus gapped extensions.\"},{\"question\":\"What metrics are used to summarize results for each protein family?\",\"answer\":\"The tables include SWISS-PROT accession identifiers, low E-value counts (with stated thresholds), alignment scores for Smith–Waterman, BLAST variants, and PSI-BLAST, as well as an average summary and normalized running time.\"}]","Protein Homology Search Performance Comparison - 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