Investigation of ionospheric anomalies during equatorial and low latitude is of major concern for modeling and global navigation satellite system (GNSS) applications. Total electron content (TEC) varies with the ionospheric conditions, which will lead to the errors in the global positioning system (GPS) measurements. It is therefore a method that is necessary to characterize the ionospheric anomalies for satellite-based navigation systems. In this study, characterization of ionospheric variations based on the singular value decomposition (SVD) and classical multidimensional scaling (MDS) methods was studied. The yearly and daily variations are decomposed from the GPS-TEC, international reference ionosphere (IRI) 2007 and IRI 2012 models TEC over the three low-latitude GNSS stations located at Koneru Lakshmaiah University (KLU-Guntur), Hyderabad and Bangalore, respectively. From the results, it is found that there is a strong correlation between GPS-TEC and IRI models. The correlation coefficient for the first three singular values is more than 0.86. From this, it is possible to reconstruct more than 85 % of the variability contained in global GPSderived VTEC data (for year 2013) by using only the first three modes. The semiannual variation has maximum value during March-April and September-October and has minimum value during June-July. It is observed that the annual variations have maximum value in summer and minimum value in winter, and the amplitudes decrease with increasing latitude. Further, opposite latitudinal asymmetry among annual and semiannual variations for three GNSS stations is noticed. SVD and MDS methods clearly show time-varying characteristics and the absence of the winter anomaly at low-latitude GNSS stations.