Editing Sequence database (section)

== Current issues ==

=== Storage & redundancy ===
Records in sequence databases are deposited from a wide range of sources, from individual researchers to large genome sequencing centers.  As a result, the sequences themselves, and especially the biological annotations attached to these sequences, may vary in quality.  There is much redundancy, as multiple labs may submit numerous sequences that are identical, or nearly identical, to others in the databases.<ref name="Sikic-2010">{{Cite journal  | last1 = Sikic | first1 = K. | last2 = Carugo | first2 = O. | title = Protein sequence redundancy reduction: comparison of various method | journal = Bioinformation | volume = 5 | issue = 6 | pages = 234–9 | year = 2010 | doi =  10.6026/97320630005234| pmid = 21364823 | pmc=3055704}}</ref>

Many annotations of the sequences are based not on laboratory experiments, but on the results of sequence similarity searches for previously annotated sequences.  Once a sequence has been annotated based on similarity to others, and itself deposited in the database, it can also become the basis for future annotations.  This can lead to a ''transitive annotation problem'' because there may be several such annotation transfers by sequence similarity between a particular database record and actual [[wet lab]] experimental information.<ref name="Iliopoulos-2003">{{Cite journal  | last1 = Iliopoulos | first1 = I. | last2 = Tsoka | first2 = S. | last3 = Andrade | first3 = MA. | last4 = Enright | first4 = AJ. | last5 = Carroll | first5 = M. | last6 = Poullet | first6 = P. | last7 = Promponas | first7 = V. | last8 = Liakopoulos | first8 = T. | last9 = Palaios | first9 = G. | last10 = Pasquier | first10 = C | last11 = Hamodrakas | first11 = S | last12 = Tamames | first12 = J | last13 = Yagnik | first13 = A. T. | last14 = Tramontano | first14 = A | last15 = Devos | first15 = D | last16 = Blaschke | first16 = C | last17 = Valencia | first17 = A | last18 = Brett | first18 = D | last19 = Martin | first19 = D | last20 = Leroy | first20 = C | last21 = Rigoutsos | first21 = I | last22 = Sander | first22 = C | last23 = Ouzounis | first23 = C. A. | title = Evaluation of annotation strategies using an entire genome sequence | journal = Bioinformatics | volume = 19 | issue = 6 | pages = 717–26 |date=April 2003 | doi =  10.1093/bioinformatics/btg077| pmid = 12691983 | display-authors = 8 | doi-access = free }}</ref> Therefore, care must be taken when interpreting the annotation data from sequence databases.

=== Scoring methods ===
Most of the current database search algorithms rank alignment by a score, which is usually a particular scoring system.<ref>{{cite journal |title=Issues in searching molecular sequence databases|last1=Altschul |first1=Stephen |last2=Boguski |first2=Mark |last3=Gish |first3=Warren |last4=Wootton |first4=John |journal=Nature Genetics |year=1994 |volume=6 |issue=2 |pages=119–129 |url=https://www.nature.com/articles/ng0294-119.pdf |publisher=Nature Publishing Group|doi=10.1038/ng0294-119 |pmid=8162065 |s2cid=270160 }}</ref> The solution towards solving this issue is found by making a variety of scoring systems available to suit to the specific problem.

=== Alignment statistics ===
When using a searching algorithm we often produce an ordered list which can often carry a lack of biological significance.<ref>{{cite journal |title=Issues in searching molecular sequence databases|last1=Altschul |first1=Stephen |last2=Boguski |first2=Mark |last3=Gish |first3=Warren |last4=Wootton |first4=John |journal=Nature Genetics |year=1994 |volume=6 |issue=2 |pages=119–129 |url=https://www.nature.com/articles/ng0294-119.pdf |publisher=Nature Publishing Group|doi=10.1038/ng0294-119 |pmid=8162065 |s2cid=270160 }}</ref>