Analysis of slipped sequences in EST projects.
نویسندگان
چکیده
Slippage is an important sequencing problem that can occur in EST projects. However, very few studies have addressed this. We propose three new methods to detect slippage artifacts: arithmetic mean method, geometric mean method, and echo coverage method. Each method is simple and has two different strategies for processing sequences: suffix and subsequence. Using the 291,689 EST sequences produced in the SUCEST project, we performed comparative tests between our proposed methods and the SUCEST method. The subsequence strategy is better than the suffix strategy, because it is not anchored at the end of the sequence, so it is more flexible to find slippage at the beginning of the EST. In a comparison with the SUCEST method, the advantage of our methods is that they do not discard the majority of the sequences marked as slippage, but instead only remove the slipped artifact from the sequence. Based on our tests the echo coverage method with subsequence strategy shows the best compromise between slippage detection and ease of calibration.
منابع مشابه
Analysis of slipped sequences in ESTs Projects
Slippage is an important sequencing problem that can occur in EST projects. However, there are very few studies about it. In this work we propose three new methods to detect slippage artifacts: “Arithmetic Mean Method”, “Geometric Mean Method”, and “Echo Coverage Method”. Each method is simple and has two different strategies for processing sequences: suffix and subsequence. Using the 291689 ES...
متن کاملExpressed Sequence Tags as a Tool for Phylogenetic Analysis of Placental Mammal Evolution
BACKGROUND We investigate the usefulness of expressed sequence tags, ESTs, for establishing divergences within the tree of placental mammals. This is done on the example of the established relationships among primates (human), lagomorphs (rabbit), rodents (rat and mouse), artiodactyls (cow), carnivorans (dog) and proboscideans (elephant). METHODOLOGY/PRINCIPAL FINDINGS We have produced 2000 E...
متن کاملP-215: Discovery of A Novel APA Variant of A Human Potential Gene Based on Expressed Sequenced Tags Analysis
Background: Expressed sequence tags (ESTs) are sequences of cDNA fragments prepared from different tissue sources. There are over one million of these sequences in the publicly available database, and these sequences are believed to represent more than half of all human genes. The ESTs belong to different cDNA libraries, was prepared from one particular cell type, organ, or tumor. Therefore, th...
متن کاملCR-EST: a resource for crop ESTs
The crop expressed sequence tag database, CR-EST (http://pgrc.ipk-gatersleben.de/cr-est/), is a publicly available online resource providing access to sequence, classification, clustering and annotation data of crop EST projects. CR-EST currently holds more than 200,000 sequences derived from 41 cDNA libraries of four species: barley, wheat, pea and potato. The barley section comprises approxim...
متن کاملESTpass: a web-based server for processing and annotating expressed sequence tag (EST) sequences
We present a web-based server, called ESTpass, for processing and annotating sequence data from expressed sequence tag (EST) projects. ESTpass accepts a FASTA-formatted EST file and its quality file as inputs, and it then executes a back-end EST analysis pipeline consisting of three consecutive steps. The first is cleansing the input EST sequences. The second is clustering and assembling the cl...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید
ثبت ناماگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید
ورودعنوان ژورنال:
- Genetics and molecular research : GMR
دوره 5 1 شماره
صفحات -
تاریخ انتشار 2006