Protein sequences of the genes spanning from Phvul.002G200900.1 to Phvul.002G202200.1 on the bean genome sequence were used as query in Bl2seq to detect most similar sequences in the sequenced genomes of G. max, C. arietinum and M. truncatula.
In single linkage, it is the similarity between the two most similar sequences; in complete linkage, between the two most dissimilar sequences; and in average linkage, the average of all pairwise similarities.
Although the capsid protein of SsHADV-1 lacks sequence similarity with those of any geminiviruses, its most similar sequences are commonly found in environmental samples.
We recorded species designations of the first three most similar sequences, which in all cases showed a similarity of more than 99.1% (average BLAST bitscore of 1095 ± 4.31 SEM).
We constructed a control sequence set for each patient by submitting each sequence of the patient to a BLAST search and selecting from the BLAST result list (ordered in descending similarity score) a fixed number of the most similar sequences of appropriate length.
A BLAST (http://blast.ncbi.nlm.nih.gov/Blast.cgi) search retrieved such highly similar genes only from Y. pestis sequences; the next most similar sequences of other Enterobacteriaceae were at 78% similarity.
Most of them rely on sequence similarity between genes where function and homology are assessed from the most similar sequences [ 22].
The most similar sequences to the sequence of the isolated strain were obtained using BLAST similarity search tool, and the multiple sequence alignment was performed using the program MUSCLE by progressive alignment method.
It may be performed either explicitly, e.g. to find the most similar sequences in a database, or implicitly as a hidden building block of more complex methods, e.g. for reads mapping.
