# US 2013/0158880 A1 · Analysis of Community Structures in Environmental Samples > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 2013/0158880 A1 - Document ID: US20130158880A1 - Status: Published application - Kind: A1 - Application number: 13/331,557 - Filed: 2011-12-20 - Published: 2013-06-20 - Earliest claimed: 2011-12-20 - Assignees: Tata Consultancy Services Limited - Inventors: Sharmila Shekhar Mande; Kuntal Kumar Bhusan; Tarini Shankar Ghosh - Web page: https://patentgrep.com/patent/US20130158880A1 ## CPC - G16B 45/00: ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks - G16B 10/00: ICT specially adapted for evolutionary bioinformatics, e.g. phylogenetic tree construction or analysis - G16B 25/10: Gene or protein expression profiling; Expression-ratio estimation or normalisation - G16B 50/30: Data warehousing; Computing architectures - G06T 11/26: Drawing of charts or graphs - G16B 25/00: ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression - G16B 50/00: ICT programming tools or database systems specially adapted for bioinformatics - G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY - G06T: IMAGE DATA PROCESSING OR GENERATION, IN GENERAL ## Abstract Systems and methods for analyzing community structures within a plurality of environmental samples are described herein. The method includes obtaining taxa data corresponding to taxonomic groups within the plurality of the environmental samples. Based on the taxa data, an abundance value for each of the taxonomic groups with respect to each of the plurality of environmental samples is determined. Further, based on abundance values, an interaction factor for each pair of the taxonomic groups in the plurality of environmental samples is computed. The interaction factor is indicative of a degree of interaction between a pair of taxonomic groups from among the taxonomic groups. Based in part on interaction factors and abundance values, the plurality of the environmental samples is clustered. ## Claims ### Claim 1 A method for analyzing community structures within a plurality of environmental samples, the method comprising: obtaining taxa data corresponding to taxonomic groups within the plurality of the environmental samples; determining an abundance value for each of the taxonomic groups with respect to each of the plurality of environmental samples, based on the taxa data; computing an interaction factor for each pair of the taxonomic groups in the plurality of environmental samples based on corresponding abundance values, wherein the interaction factor is indicative of a degree of interaction between a pair of taxonomic groups from among the taxonomic groups; and clustering the plurality of the environmental samples based in part on interaction factors and abundance values. ### Claim 2 (depends on 1) The method as claimed in claim 1, wherein the clustering further comprises generating a community structure analysis profile indicative of the clustering of the plurality of environmental samples. ### Claim 3 (depends on 1) The method as claimed in claim 1, wherein the determining further comprises normalizing the abundance value for each of the taxonomic groups based on a size of a corresponding environmental sample. ### Claim 4 (depends on 3) The method as claimed in claim 3, wherein the size of the corresponding environmental sample denotes one of a total number of assigned sequences in the corresponding environmental sample, and a total number of operational taxonomic units (OTUs) obtained for the corresponding environmental sample. ### Claim 5 (depends on 1) The method as claimed in claim 1, wherein computing the interaction factor for each pair of the taxonomic groups comprises: determining a correlation coefficient between the pair of taxonomic groups based on the abundance values corresponding to the taxonomic groups constituting the pair; and computing a correlation distance corresponding to the pair based on the correlation coefficient to obtain the interaction factor for the pair. ### Claim 6 (depends on 2) The method as claimed in claim 2, wherein the generating further comprises creating a taxa interaction profile based on the interaction factors. ### Claim 7 (depends on 6) The method as claimed in claim 6, wherein creating the taxa interaction profile comprises generating a linear arrangement of taxonomic groups in a two dimensional space. ### Claim 8 (depends on 1) The method as claimed in claim 1, wherein the clustering further comprises determining a force factor corresponding to each of the plurality of the environmental samples, based on the taxa interaction profile. ### Claim 9 (depends on 8) The method as claimed in claim 8, wherein the force factor of each of the plurality of the environmental samples is based in part on the abundance value for each of taxonomic groups and the taxa interaction profile. ### Claim 10 A community structure analysis (CSA) system comprising: a processor; and a memory coupled to the processor, the memory comprising: a taxa interaction module configured to, determine an abundance value for each of taxonomic groups with respect to each of a plurality of environmental samples; and compute an interaction factor for each pair of the taxonomic groups in the plurality of environmental samples, based in part on abundance values, wherein the interaction factor is indicative of a degree of interaction between a pair taxonomic groups from among the taxonomic groups; and a community structure (CS) analysis module configured to, create a taxa interaction profile based on the interaction factors, wherein the taxa interaction profile is indicative of interactions among the taxonomic groups; and generate a community structure analysis profile based on the taxa interaction profile, wherein the community structure analysis profile is indicative of clustering of the plurality of the environmental samples. ### Claim 11 (depends on 10) The CSA system as claimed in claim 10, wherein the CS analysis module is further configured to: select a taxonomic group from the taxonomic groups; associate a rank with each of remaining taxonomic groups based on the interaction factors corresponding to each of the remaining taxonomic groups with respect to the selected taxonomic group; and cluster the taxonomic groups based on ranks to create the taxa interaction profile. ### Claim 12 (depends on 10) The CSA system as claimed in claim 10, wherein the CS analysis module is further configured to: determine a center of taxonomic alignment based on the taxa interaction profile; compute an initial position corresponding to each of the plurality of the environmental samples based in part on one or more dimensional parameters and the center of taxonomic alignment; determine a force factor corresponding to each of the plurality of the environmental samples based in part on the initial position of the corresponding environmental sample and the taxa interaction profile, wherein the force factor is representative of combined interaction pattern of constituent taxonomic groups within the corresponding environmental sample; and compute a final position corresponding to each of the plurality of the environmental samples based on the corresponding force factor to generate the community structure analysis profile. ### Claim 13 (depends on 12) The CSA system as claimed in claim 12, wherein the CS analysis module is further configured to: determine a force vector on each of the plurality of the environmental samples due to each of the taxonomic groups; and compute the force factor for each of the plurality of the environmental samples based on a cumulative sum of corresponding force vectors. ### Claim 14 A computer-readable medium having embodied thereon a computer program for executing a method for vehicle allocation and routing, the method comprising: determining an abundance value for each of taxonomic groups with respect to each of a plurality of environmental samples based on a taxonomic summary file associated with a corresponding environmental sample; computing an interaction factor for each pair of the taxonomic groups in the plurality of environmental samples, based on abundance values; creating a taxa interaction profile based on interaction factors, wherein the taxa interaction profile is indicative of interactions among the taxonomic groups; and generating a community structure analysis profile based in part on the taxa interaction profile, wherein the community structure analysis profile is indicative of a comparative representation of the community structures within the plurality of environmental samples. ### Claim 15 (depends on 14) The computer-readable medium as claimed in claim 14, wherein the determining further comprises normalizing the abundance value for each of the taxonomic groups based on a size of a corresponding environmental sample. ### Claim 16 (depends on 14) The computer-readable medium as claimed in claim 14, wherein computing the interaction factor for each pair of the taxonomic groups comprises: determining a correlation coefficient between the pair of taxonomic groups based on the abundance values corresponding to the taxonomic groups constituting the pair; and computing a correlation distance corresponding to the pair based on the correlation coefficient to obtain the interaction factor for the pair. ### Claim 17 (depends on 14) The computer-readable medium as claimed in claim 14, wherein creating the taxa interaction profile comprises generating a linear arrangement of taxonomic groups in a two dimensional space. ### Claim 18 (depends on 14) The computer-readable medium as claimed in claim 14, wherein creating the taxa interaction profile comprises: selecting a taxonomic group from the taxonomic groups; associating a rank with each of remaining taxonomic groups based on the interaction factors corresponding to each of the remaining taxonomic groups with respect to the selected taxonomic group; and clustering the taxonomic groups based on ranks to create the taxa interaction profile. ### Claim 19 (depends on 14) The computer-readable medium as claimed in claim 14, wherein the generating comprises; computing an initial position corresponding to each of the plurality of the environmental samples based in part on one or more dimensional parameters and the center of taxonomic alignment; determining a force factor corresponding to each of the plurality of the environmental samples based in part on the initial position of the corresponding environmental sample and the taxa interaction profile, wherein the force factor is representative of combined interaction pattern of constituent taxonomic groups within the corresponding environmental sample; and computing a final position corresponding to each of the plurality of the environmental samples based on the corresponding force factor to generate the community structure analysis profile.