Crossword Puzzle

2. method used in sequence alignment to assess the probability that an observed alignment score occurred by chance in database searches (E-VALUE).
4. approach that breaks DNA sequence searches into smaller overlapping words for faster database scanning, used in BLAST (WORD METHOD).
6. tool used for predicting protein domains and functional sites based on profile hidden Markov models (PFAM).
7. method that predicts the secondary structure of RNA sequences by minimizing free energy (MFOLD).
9. that provides 3D macromolecular structure data obtained via X-ray crystallography, NMR, and cryo-EM (PDB).
11. software pipeline for analyzing RNA-Seq data, aligning reads to the genome, and quantifying gene expression (TOPHAT).
12. model used in gene prediction and sequence alignment that incorporates transition probabilities between hidden states (HMM).
14. sequence database that combines information from Swiss-Prot, TrEMBL, and PIR databases (UNIPROT).

1. assembly approach that constructs graphs representing overlaps between sequence reads (DE BRUIJN GRAPH).
3. used for optimal global sequence alignment, considering all positions in two sequences (NEEDLEMAN–WUNSCH).
4. used for reconstructing phylogenetic trees by minimizing the total number of evolutionary changes (PARSIMONY).
5. database storing nucleotide sequences from more than 100,000 organisms, maintained by NCBI (GENBANK).
8. of evolutionary distance between sequences based on the expected number of substitutions per site (KIMURA DISTANCE).
10. sequence alignment algorithm that uses progressive alignment and hierarchical clustering to align homologous sequences (CLUSTALW).
13. of sequence motif represented by a matrix of nucleotide or amino acid probabilities at each position (POSITION WEIGHT MATRIX).