Patent ID: 6871147
Filing Date: 2005-03-22
Classification: G16B,Y10S

Abstract:
1. A method of obtaining and organizing information about a plurality of unknown raw nucleic acid sequences, comprising: a) creating a directory of files in a computer, for storing information related to the plurality of unknown raw nucleic acid sequences; b) inputting the plurality of unknown raw nucleic acid sequences into the computer; c) automatically determining trimming locations of each unknown raw nucleic acid sequence using a best match type scoring algorithm which, during each scoring operation, assigns a nucleotide paired with a matching nucleotide a highest value, assigns a nucleotide paired with an unidentified nucleotide an intermediate value and assigns a nucleotide paired with a mismatched nucleotide a lowest value and which, during each scoring operation, allows either a single nucleotide insertion or a single nucleotide deletion in the unknown raw nucleic acid sequence, the scoring algorithm first comparing a known positive 5′ adapter sequence and a known negative 5′ adapter sequence to the raw nucleic acid sequence and assigning a 5′ trimming location to a position in the unknown raw nucleic acid sequence having the highest score and determining an insertion orientation according to the higher scoring of the known positive and negative 5′ adapter sequences, then comparing a known 3′ adapter sequence having a same orientation as the higher scoring known 5′ adapter sequence to the unknown raw nucleic acid sequence and assigning a 3′ trimming location to a position in the unknown raw nucleic acid sequence having the highest score, then comparing a known positive confirmation sequence and a known negative confirmation sequence to the raw nucleic acid sequence and assigning a confirmation sequence location to a position in the unknown raw nucleic acid sequence having the highest score and determining a sequencing direction according to the higher scoring of the known positive and negative confirmation sequences, and then trimming each of the plurality of unknown raw nucleic acid sequences to obtain a respective plurality of trimmed unknown nucleic acid sequences; d) submitting each of the plurality of trimmed unknown nucleic acid sequences electronically to a nucleic acid identification database having a search program, the search program producing search results based on similarity of a trimmed unknown nucleic acid sequence to a known nucleic acid sequence, and receiving the search results for each of the plurality of trimmed unknown nucleic acid sequences electronically from the nucleic acid identification database; e) automatically choosing selective information, including similar known nucleic acid sequences, from each search result and automatically inserting the selective information from each search result into a respective first electronic spreadsheet; f) selecting at least one of the search results from each of the respective first electronic spreadsheets and automatically inserting the selective information about the at least one search result into a second electronic spreadsheet.