Q. In sequence alignment by BLAST, each word from query sequence is typically _______ residues for protein sequences and _______ residues for DNA sequences.

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Q. In sequence alignment by BLAST, the second step is to search a sequence database for the occurrence of these words.

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Q. The final step involves pairwise alignment by extending from the words in both directions while counting the alignment score using the same substitution matrix.

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Q. A recent improvement in the implementation of BLAST is the ability to provide gapped alignment.

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Q. Which of the following is not a variant of BLAST?

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Q. BLASTX uses protein sequences as queries to search against a protein sequence database.

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Q. TBLASTX queries protein sequences to anucleotide sequence database with the sequences translated in all six reading frames.

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Q. Which of the following is not correct about BLAST?

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Q. If one is looking for protein homologs encoded in newly sequenced genomes, one may use TBLASTN, which translates nucleotide database sequences in all six open reading frames.

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Q. Which of the following is not correct about FASTA?

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Q. The first step in FASTA alignment id to arrange the sequences in matrices’ rows and columns in order to be analyzed.

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Q. The positional difference for each word between the two sequences is obtained by ________ the position of the ______ sequence from that of the _______ sequence and is expressed as the offset.

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Q. The second step in FASTA is to narrow down the high similarity regions between the two sequences.

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Q. In FASTA, neighboring high-scoring segments along the same diagonal are selected and joined to form a single alignment.

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Q. The last step is to perform a statistical evaluation of the final alignment as in BLAST, which produces the E-value.

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Q. The web-based FASTA program is offered by the European Bioinformatics Institute.

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Q. FASTX, which compares a protein query sequence to a translated DNA database.

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Q. FASTA doesn’t use bit scores.

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Q. Z-score describes the number of standard deviations from the mean score for the database search.

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Q. In FASTA, For a Z-score > 15, the match can be considered extremely ______ with _____ of a homologous relationship.

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